1002/prot. Re: Langevin process in NAMD tutorial" Previous message: Basak Isin: "Re: Regarding answering questions in a forum. washington. 5923 Kcal/mol also we have 6. edu> wrote: > I would like to calculate the free energy of a protein-protein complex using > the Jarzinsky's equation from already performed SMD simulations. UW Bioengineering announces that Barry Lutz is hired as tenure-track faculty, Gianluca Interlandi joins faculty and Suzie Pun is promoted to full professorIn reply to: Gianluca Interlandi: "NAMD + nice" Messages sorted by: [ attachment ] Nice (process priority) is only supported in NET version of Charm++. edu> Cc: <namd-l_at_ks. From: Stern, Julie (jvstern_at_bnl. Just source the Tcl file and use the 'unwrap' procedure. washington. edu) Date: Fri May 04 2007 - 17:53:42 CDT Next message:. In reply to: Gianluca Interlandi: "Vibrational mode analysis" Next in thread: Richard Law: "Re: Vibrational mode analysis" Messages sorted by: [ attachment ] CHARMM does normal mode. Re: Protein in/out of box. Gianluca Interlandi Curriculum Vitae Department of Bioengineering, University of Washington, 1705 NE Pacific Street, 98195 Seattle, WA, [email protected]> wrote: >>> if you want to go low risk and don't have much experience with GPU, then >>> probably the best deal you can currently get for running NAMD on small On Wed, 16 Sep 2020 at 11:40, Gianluca Interlandi <gianluca_at_u. edu> > I suspect that E3_19 might not be stable with this type of implicit solvent > model (it doesn't contain a term to take the non-polar solvation energy into > accout). Neil King Assistant Professor. edu> wrote: > Dear all, > > Does anybody have any recommendation how to convert a solvated system > (protein + solvent + ions) PDB + PSF from the CHARMM to the Amber force > field so that it can be used in NAMD with the. It's > slightly faster but still not that much faster than running on 16 CPU cores. edu> wrote: > Hi Fatemeh, > > Thanks for replying. prm". washington. I doubt that there is a way to have> 2011/6/29 Gianluca Interlandi <gianluca_at_u. washington. Does Berendsen increase viscosity of water? From: Gianluca Interlandi (gianluca_at_u. Hemostasis in vertebrates involves both a. Is it still possible to apply Jarzinsky's equation? > Also, according to your publication I have to integrate the work done along the. In the text > field you can enter your atom selection, e. You should simulate it in explicit water (or try one of the implicitRe: Protein in/out of box. 15 K 1 KT = 2. edu]Reply All Saturday,. edu) Date: Thu Sep 21 2006 - 16:55:46 CDT Next message: jonathan_at_ibt. > On Wed, 16 Sep 2020 at 11:40, Gianluca Interlandi <gianluca_at_u. washington. Research Assistant Professor (Independent Lab) e-mail: gianluca@u. VMD-L Mailing List. washington. It's > slightly faster but still not that much faster than running on 16 CPU cores. I doubt that there is a way to have> On Thu, Apr 7, 2011 at 2:22 PM, Gianluca Interlandi > <gianluca_at_u. Cheers, Johan On Thu, Apr 7, 2011 at 4:40 PM, Gianluca InterlandiHosted by Gianluca Interlandi Ask a question. Write a review. edu) Date: Mon Oct 11 2010 - 16:56:03 CDT Next message: Basak Isin: "Re: Regarding answering questions in a forum. 6 ns/day for a 100k atom system with roughly those same parameters (and. washington. But if you simulate entire proteins, charged termini. edu> wrote: > With multicore I get 96 sec per 1000 steps from the Benchmark time. Next in thread: Gianluca Interlandi: "Re: NAMD 2. Is it still possible to apply Jarzinsky's equation? > Also, according to your publication I have to integrate the work done along the. Gianluca On Thu, 31 May 2012, Kapil jain wrote: > Hi all, > I am running md simulation on homology model of a membrane protein, following the membrane > protein tutorial. edu> > I suspect that E3_19 might not be stable with this type of implicit solvent > model (it doesn't contain a term to take the non-polar solvation energy into > accout). edu> Date: Monday, May 7, 2007 7:26 pm Subject: Re: namd-l: query about wrapped coordinates > I have actually found a much easier way of adding the crystal > information > to your trajectory. It's > slightly faster but still not that much faster than running on 16 CPU cores. washington. edu) Date: Wed May 06 2009 - 11:04:21 CDT Next message: Anton Arkhipov: "Re: Langevin damping coefficient" Previous message: Benjamin Stauch: "diffusion / fex peptide problem" In reply to: Anton Arkhipov: "Re: Langevin damping coefficient" Gianluca On Mon, 11 Apr 2011, Axel Kohlmeyer wrote: > On Mon, Apr 11, 2011 at 3:41 PM, Gianluca Interlandi > <gianluca_at_u. In reply to: Gianluca Interlandi: "Re: Changing Boundary conditions from PBC to non-periodic" Messages sorted by: [ attachment ] How would somebody want to simulate explicit water molecules without PBC? The water molecules will quickly diffuse and your protein be in vacuum. washington. washington. > > Gianluca > > > On Thu, 12 Jul 2012, Aron Broom wrote: > > have you tried the multicore build? On Thu, Jul 12, 2012 at 3:53 PM, Gianluca Interlandi < gianluca_at_u. edu> wrote: > I would like to calculate the free energy of a protein-protein complex using > the Jarzinsky's equation from already performed SMD simulations. edu] Sent: Monday, June 20, 2016 12:46 PM To: Richard Wood Cc: John Stone; vmd-l_at_ks. Is it still possible to apply Jarzinsky's equation? > Also, according to your publication I have to integrate the work done along the. I > > attach a plot of a constant velocity simulation where I'm pulling twoRe: NAMD 2. edu) Date: Thu Jun 15 2006 - 21:01:04 CDT Next message: Taeho Kim: "free energy calculate" Previous message: L. -Fatemeh On Fri, Dec 3, 2010 at 2:08 PM, Gianluca Interlandi < gianluca_at_u. Gianluca Interlandi Curriculum Vitae Department of Bioengineering, University of Washington, 1705 NE Pacific Street, 98195 Seattle, WA, [email protected] on Abe" In reply to: Gianluca Interlandi: "Re: Yet another NAMD speed concerns" Messages sorted by: [ attachment ] The amount of computational work that you have for the nonbonded short-range interactions (which is the dominant part of the overallConvert solvated CHARMM PDB + PSF to Amber. I also ran a non-CUDA job on Forge > using 16 CPUs. washington. edu on behalf of Gianluca Interlandi [gianluca_at_u. The bacterial adhesin FimH is a model for the study of protein allostery because its structure has been resolved in multiple configurations, including the active and the inactive state. VMD-L Mailing List. washington. , "not. One of the. Eddie: "gentoo ebuild" Previous message: Robert Johnson: "Re: ABF/Steered MD for DNA Hybridization on Carbon Nanotubes" Maybe in reply to: Norman Geist: "AW: AW: Running NAMD on Forge (CUDA)"Gianluca Interlandi, ‡, 1, 2 Olga Yakovenko, ‡, 1 An-Yue Tu,. SMD on center of mass. From: Buddhadev Maiti (bmaiti_at_gsu. washington. In the NAMD folder that you downloaded there >> is a file called "notes. You should simulate it in explicit water (or try one of the implicitGianluca, Looking at the code, it does not, but that would be easy to adapt from the NAMD's ComputeCrossterms. I would like to erase Windows and install Leap 42. washington. edu Phone: (206)685-4435 Office: Foege N430 E Gianluca Interlandi I am interested in understanding at molecular level the function of proteins involved in hemostasis and thrombosis, and how they interact with each other and with material surfaces. washington. Re: NAMD 2. washington. edu) Date: Thu Apr 05 2012 - 17:04:15 CDT Next message: Gianluca Interlandi: "multicore versus net-linux" Previous message: Gianluca Interlandi: "RE: DCD" In reply to: Gianluca Interlandi: "RE: DCD" Next in thread: Buddhadev Maiti: "RE: DCD"From: Gianluca Interlandi (gianluca_at_u. edu) Date: Thu Jun 15 2006 - 21:01:04 CDT Next message: Taeho Kim: "free energy calculate" Previous message: L. edu> > I suspect that E3_19 might not be stable with this type of implicit solvent > model (it doesn't contain a term to take the non-polar solvation energy into > accout). Swett wrote: > From your email, it's apparent that you are in > the pharmacy school of the university of maryland. From: Gianluca Interlandi (gianluca_at_u. washington. 7 released" Messages sorted by: [ attachment ] Thank you very much! It seems to be up to 40% faster than the 2. edu> > wrote: > are other people also using those GPUs? > > Previous message: Gianluca Interlandi: "Conversion for forces" In reply to: Gianluca Interlandi: "Conversion for forces" Next in thread: Gianluca Interlandi: "SMD and restart" Reply: Gianluca Interlandi: "SMD and restart" Messages sorted by: [ attachment ] This archive was generated by Research Assistant Professor gianluca@u. edu) Date: Thu Nov 02 2006 - 21:27:41 CST Next message: Dhiraj Srivastava: "production in NVE ensemble after equilibration in NPT ensemble" Previous message: Gianluca Interlandi: "Re: SMD on center of mass" In reply to: Gianluca Interlandi: "Re: SMD on center of mass" In reply to: Gianluca Interlandi: "Re: Jarzinsky's equation" Messages sorted by: [ attachment ] If that's the only force you are applying to the system, then that is your external work. The difference is usually after the > 4th decimal after the period. washington. Gianluca Interlandi 1 Affiliation 1 Department of Bioengineering, University of Washington, Seattle, Washington, USA. > > On Thu, Jul 12, 2012 at 3:21 PM, Gianluca Interlandi > <gianluca_at_u. washington. I thought that free Dagmara I. We are building a smaller cluster though in the lab and will test the scalabilityGianluca On Mon, 11 Apr 2011, Axel Kohlmeyer wrote: > On Mon, Apr 11, 2011 at 3:41 PM, Gianluca Interlandi > <gianluca_at_u. Display options. edu> wrote: > With multicore I get 96 sec per 1000 steps from the Benchmark time. That's why one wants to use a low value for the damping constant, in principle. edu) Date: Thu Feb 20 2014 - 13:15:51 CST Next message: zeynab mohamad hoseyni: "FATAL ERROR: EOF ENCOUNTERED READING CROSS-TERMS FROM PSF FILE" Previous message: Kenno Vanommeslaeghe: "Re: tools for Charmm" In reply to: Kenno Vanommeslaeghe: "Re:. edu> > wrote: > Roy, > > I think that you are confusing two things. 100% refund of amount payable if you cancel at least 14 days before check-in. Maybe the file was not transferred correctly to your desktop PC. washington. RE: Force field design. You simply load your trajectory > > into VMD On 7/7/2011 6:08 PM, Gianluca Interlandi wrote: > Francesco, > > Just a hint. From: Gianluca Interlandi (gianluca_at_u. From: Gianluca Interlandi (gianluca_at_u. Gianluca On Thu, 6 Jan 2011, Gianluca Interlandi wrote: > Hi!In reply to: Gianluca Interlandi: "Re: Question about equilibration" Next in thread: Gianluca Interlandi: "Re: Question about equilibration" Reply: Gianluca Interlandi: "Re: Question about equilibration" Messages sorted by: [ attachment ] Because an X-ray is assumed to be a structure at "zero K" and an MD equilibrated. What are you trying to accomplish?Previous message: Gianluca Interlandi: "Re: SSD vs SSHD vs mechanical" In reply to: Gianluca Interlandi: "Re: SSD vs SSHD vs mechanical" Next in thread: Axel Kohlmeyer: "Re: SSD vs SSHD vs mechanical" Messages sorted by: [ attachment ] At present I don't think NAMD will let you write a jsLe mardi 3 octobre 2006 01:01, Gianluca Interlandi a écrit : > I am performing a simulation of a complex consisting of two proteins. From: Gianluca Interlandi (gianluca_at_u. washington. washington. 7 with the PLUMED patch" Messages sorted by: [ attachment ] I found the problem. washington. uiuc. washington. 7 with the PLUMED patch. Cheers, Johan On Thu, Apr 7, 2011 at 4:40 PM, Gianluca Interlandi> 2011/6/29 Gianluca Interlandi <gianluca_at_u. edu> wrote: > Hi, > > Can the current version of NAMD be used together with the new CHARMM36 force > field? The parameter files are "top_all36_prot. Re: Yet another NAMD speed concerns. washington. 7b1)" Previous message: Christopher Hartshorn: "Re: FEP tutorial graph question" In reply to: Peter Freddolino:. Gianluca Interlandi 1 Affiliation 1 Department of Bioengineering, University of Washington, Seattle, Washington, USA. From: Gianluca Interlandi (gianluca_at_u. SASA in NAMD is used > internally to perform simulations in implicit solvent, whereas SASA in > VMD is used to analyse trajectories. From: Victor Kwan (vkwan8_at_uwo. washington. But, using the PBC my protein is continuous. washington. uiuc. UW Bioengineering announces that Barry Lutz is hired as tenure-track faculty, Gianluca Interlandi joins faculty and Suzie Pun is promoted to full professorGianluca Interlandi's 67 research works with 730 citations and 2,578 reads, including: Rate limiting step of the allosteric activation of the bacterial adhesin FimH investigated by. Citat Gianluca Interlandi <gianluca_at_bioc. From: John Stone (johns_at_ks. washington. On Fri, 9 Feb 2007, Gianluca Interlandi wrote: > Dear Marcos, > > Thanks a lot for your answer and for offering me your help. > > On Thu, Jul 12, 2012 at 3:21 PM, Gianluca Interlandi <gianluca_at_u. edu Subject: RE: vmd-l: Can't read DCD files generated using NAMD. rtf" and "par_all36_prot. Re: Vibrational mode analysis. washington. washington. Location info. com) Date: Fri Aug 30 2013 - 18:19:04 CDT Next message: Gianluca Interlandi: "Re: editing the code of the non bonded pair potentials" Previous message: Gianluca Interlandi: "Re: editing the code of the non bonded pair potentials" In reply to:. washington. Gianluca On Mon, 11 Apr 2011, Axel Kohlmeyer wrote: > On Mon, Apr 11, 2011 at 3:41 PM, Gianluca Interlandi > <gianluca_at_u. I needed to install the 'patch' program. edu) Date: Thu Mar 17 2011 - 17:58:46 CDT Next message: Giacomo Fiorin: "Re: GBIS and ABF" Previous message: Branko: "GBIS and ABF" In reply to: Gianluca Interlandi: "Re: NAMD 2. edu) Date: Tue Oct 17 2006 - 00:36:56 CDT Next message: Jacob Poehlsgaard: "Intel Woodcrest version?" Previous message: Jim Phillips: "Free Linux Cluster-Building Workshop - 30 Nov 2006 - 01 Dec 2006" In reply to: Gianluca Interlandi: "SMD and restart"> On Wed, Dec 1, 2010 at 1:54 AM, Gianluca Interlandi <gianluca_at_u. washington. (2010) The catch bond mechanism between von Willebrand factor and platelets investigated by molecular dynamics simulations. Reply: Gianluca Interlandi: "Re: Regarding thermostats" Reply: Marcos Sotomayor: "Re: Regarding thermostats" Messages sorted by: [ attachment ] Dear NAMD users, Lately in the lab we have been discussing about which thermostat use in our simulations. edu> wrote: > Hi Fatemeh, > > Thanks for replying. washington. On Tue, Aug 7, 2012 at 4:16 PM, Gianluca Interlandi < gianluca_at_u. com) Date: Wed Sep 18 2013 - 14:48:11 CDT Next message: Gianluca Interlandi: "Re: Open VMD from a remote host" Previous message: John Stone: "Re: Open VMD from a remote host" In reply to: Gianluca Interlandi: "Open VMD from a remote host" Next in thread: Gianluca. washington. Reply: Gianluca Interlandi: "Re: Cuda benchmarks namd2. edu) Date: Thu Jul 16 2015 - 16:20:34 CDT Next message: Simon Kit Sang Chu: "Minimization without MD" Previous message: Gianluca Interlandi: "Re: namd ibverbs" In reply to: Gianluca Interlandi: "Re: namd ibverbs" Next in thread:. , and Thomas W. 5923 Kcal/mol also we have 6. washington. edu) Date: Thu Apr 05 2012 - 17:04:15 CDT Next message: Gianluca Interlandi: "multicore versus net-linux" Previous message: Gianluca Interlandi: "RE: DCD" In reply to: Gianluca Interlandi: "RE: DCD" Next in thread: Buddhadev Maiti: "RE: DCD"Re: Langevin damping coefficient. View all 11 amenities. > > Gianluca > > On Wed, 23 Sep 2015, John Stone. by G. washington. edu) Date: Wed Jun 15 2011 - 14:18:43 CDT Next message: Reichert, David: "RE: Question about equilibration" Previous message: Richard Wood: "Re: Question about equilibration" In reply to: Richard Wood: "Re: Question about. edu> wrote: > With multicore I get 96 sec per 1000 steps from the Benchmark time. washington. PMID: 37700555; DOI: 10. Gianluca From: Gianluca Interlandi (gianluca_at_u. ca) Date: Tue Oct 31 2023 - 20:31:14 CDT Next message: Gianluca Interlandi: "Re: VMD openGL over ssh from a server with NVIDIA" Previous message: Victor Kwan: "Re: VMD openGL over ssh from a server with NVIDIA" In reply to: Gianluca Interlandi: "Re: VMD openGL over ssh from a. NAMD doesn't that i know of. com) Date: Sat Dec 04 2010 - 02:07:05 CST Next message: Gianluca Interlandi: "Re: Fwd: Installing NAMD on windows" Previous message: Gianluca Interlandi: "Re: Jarzinsky's equation" Next in thread: Gianluca Interlandi: "Re: Fwd:. I > > attach a plot of a constant velocity simulation where I'm pulling two > > proteins apart. washington. Gianluca On Thu, 31 May 2012, Kapil jain wrote: > Hi all, > I am running md simulation on homology model of a membrane protein, following the membrane > protein tutorial. Sunhwan On Jul 16, 2014, at 12:32 AM, Gianluca Interlandi <gianluca_at_u. Reply: Gianluca Interlandi: "Re: Running NAMD on Forge (CUDA)" Messages sorted by: [ attachment ] have you tried the multicore build? I wonder if the prebuilt smp one is just not working for you. >> On Wed, Dec 1, 2010 at 1:54 AM, Gianluca Interlandi <gianluca_at_u. washington. From: Gianluca Interlandi (gianluca_at_u. The server where VMD is started from has On Thu, Jul 12, 2012 at 3:53 PM, Gianluca Interlandi < gianluca_at_u. > 2011/6/29 Gianluca Interlandi <gianluca_at_u. Jennifer KongRE: DCD. Michel Espinoza-Fonseca: "Re: Vibrational. edu> > I suspect that E3_19 might not be stable with this type of implicit solvent > model (it doesn't contain a term to take the non-polar solvation energy into > accout). > On Wed, Dec 1, 2010 at 1:54 AM, Gianluca Interlandi <gianluca_at_u. At some point there will be a web page here. edu) Date: Wed Jun 15 2011 - 14:18:43 CDT Next message: Reichert, David: "RE: Question about equilibration" Previous message: Richard Wood: "Re: Question about equilibration" In reply to: Richard Wood: "Re: Question about. I have a new computer that came with Windows 10, which uses UEFI with a disk that has a GPT label. Thanks for the reply. Gianluca Interlandi, ‡, 1, 2 Olga Yakovenko, ‡, 1 An-Yue Tu,. washington. From: Gianluca Interlandi (gianluca_at_u. MyOn Wed, Dec 1, 2010 at 1:54 AM, Gianluca Interlandi < gianluca_at_u. I would be > happy if somebody could point me out to some scripts which help me performRe: Help building a desktop for namd. a, three-dimensional structure of the complex between A1 and GpIbα used in this manuscript. But not now. From: Ernesto Vargas (vargaslo_at_gmail. gov) Date: Fri Jun 18 2004 - 14:48:36 CDT Next message: Gianluca Interlandi: "Re: recentering protein in the waterbox" Previous message: Jerry Ebalunode: "recentering protein in the waterbox" Messages sorted by: [ attachment ] Hello, I'm running namd and am getting the following errors as itsIn reply to: Gianluca Interlandi: "Re: Vibrational mode analysis" Next in thread: Gianluca Interlandi: "Re: Vibrational mode analysis" Reply: Gianluca Interlandi: "Re: Vibrational mode analysis" Messages sorted by: [ attachment ] Hi Gianluca, Unfortunately I don't know from where you can get such tutorials. 478 KJ/mol = 0. how to output more significant figures in a file for energies and forces? Next message: Gianluca Interlandi: "Re: accuracy of measurement"Reply: Gianluca Interlandi: "Re: Force field design" Messages sorted by: [ attachment ] On 07/24/2014 12:03 AM, R. washington. Just source the Tcl file and use the 'unwrap' procedure. Next in thread: Gianluca Interlandi: "Re: accuracy of measurement" Reply: Gianluca Interlandi: "Re: accuracy of measurement" Messages sorted by: [ attachment ] hi namd users. Michel Espinoza-Fonseca: "Re: Vibrational mode analysis" In reply to: L. edu] Sent: Friday, June 17, 2016 2:29 PM To: Richard Wood Cc: John Stone; vmd-l_at_ks. Gianluca Interlandi. 3 hours/ns (stepsize 1, fullElectFrequency 1 and stepspercycle 20). edu > <mailto:gianluca_at_u. Next message: Gianluca Interlandi: "Infiniband and PME gridsize" Previous message: nordgren_at_sas. Facebook gives people the power to share and makes the world more open and connected. It's > slightly faster but still not that much faster than running on 16 CPU cores. washington. 6 version, although I am not running the cluster at full load yet. edu > Subject: Re: namd-l: DCD > > Load your psf+dcd into VMD. Thanks for the reply. washington. edu > Betreff: Re: namd-l: Mysterious slow down in parallel > > You should read about domain decomposition. >From: Gianluca Interlandi (gianluca_at_u. The more tasks you have the > more frequently the CPUs need to update each other. GianlucaHosted by Gianluca Interlandi. washington. edu) Date: Fri May 01 2009 - 12:18:05 CDT Next message: Grace Brannigan: "Re: crash with more than 96 processors (v2. The structure was derived from the complex co-crystallized with botrocetin (PDB code 1U0N) (), because this is the only structure of the complex where 11 amino acids of the A1 N-terminal linker were resolved (other structures. Next in thread: Gianluca Interlandi: "Re: NAMD 2. Hi I’m Yiming Li, and I’m a senior in bioengineering. 478 KJ/mol = 0. washington. One of the two proteins has reached one of > the boundaries of the box and it has been wrapped around. Re: Abe versus Lincoln. eduRe: Question about equilibration. You simply load your trajectory > into VMDReply: Gianluca Interlandi: "Re: Running NAMD on Forge (CUDA)" Messages sorted by: [ attachment ] So your speed for 1 or 2 GPUs (based on what your sent) is about 1. Reply: Gianluca Interlandi: ""wrapAll on" with a complex" Reply: Gianluca Interlandi: "Scale" Messages sorted by: [ attachment ] Dear NAMD users, I'm performing SMD simulations and I have problems when I restart a simulation, i. edu> wrote: > I would like to calculate the free energy of a protein-protein complex using > the Jarzinsky's equation from already performed SMD simulations. Be the first to write a review. From: Gianluca Interlandi (gianluca_at_u. 7 out the door on Friday. uiuc. I was getting 2. com) Date: Thu Apr 07 2011 - 14:21:33 CDT Next message: Gianluca Interlandi: "Re: Abe versus Lincoln" Previous message: Gianluca Interlandi: "Re: Abe versus Lincoln" In reply to: Gianluca Interlandi: "Re: Abe versus Lincoln" Next in thread: Gianluca Interlandi: "Re:. Does it also take account of the Urey-Bradley term? Many thanks, Gianluca ----- Gianluca Interlandi gianluca_at_bioc. Just a good MD toy ! Victor owner-namd-l_at_ks. 7 with the PLUMED patch" Next in thread: Davide Branduardi: "Re: Compiling NAMD 2. Michel Espinoza-Fonseca: "Re: Vibrational mode analysis" In reply to: L. washington. Juli 2012 00:26 > An: Aron Broom > Cc: NAMD list > Betreff: Re: namd-l: Running NAMD on Forge (CUDA) > > Yes, I was totally surprised, too. 6 : Tue Dec 27 2016 - 23:21:14 CST Gianluca Interlandi's 67 research works with 730 citations and 2,578 reads, including: Rate limiting step of the allosteric activation of the bacterial adhesin FimH investigated by molecular. washington. uiuc. washington. edu> > wrote:Previous message: Gianluca Interlandi: "Conversion for forces" In reply to: Gianluca Interlandi: "Conversion for forces" Next in thread: Gianluca Interlandi: "SMD and restart" Reply: Gianluca Interlandi: "SMD and restart" Messages sorted by: [ attachment ] kcal/mol/A^2 is actually units for a force constant (for a spring for. 7 released. > > Gianluca > > > On Thu, 12 Jul 2012, Aron Broom wrote: > > have you tried the multicore build?Gianluca Interlandi composed on 2017-01-23 13:40 (UTC-0800):. I would be > happy if somebody could point me out to some scripts which help me performHemostasis in vertebrates involves both a cellular and a protein component and von Willebrand factor evolved in the ancestral vertebrate following the divergence of the urochordates some 500 million years ago and that it acquired increasing complexity though sequential insertion of functional modules. I'm > not sure whether the CHARMM program can read. Gianluca Interlandi. 50% refund of amount payable if you cancel at least 7 days before check-in. From: Gianluca Interlandi (gianluca_at_u. 7 with the PLUMED patch" Previous message: Alex Liu: "Fix atoms-Colvars" Next in thread: Gianluca Interlandi: "Re:. edu) Date: Wed Sep 18 2013 - 13:53:55 CDT Next message: Axel Kohlmeyer: "Re: Open VMD from a remote host" Previous message: Gianluca Interlandi: "Open VMD from a remote host" In reply to: Gianluca Interlandi: "Open VMD from a remote host" Next in thread: Axel Kohlmeyer:. Try copying it again from where the simulation was run. > On Fri, 9 Feb 2007, Gianluca Interlandi wrote: > > > Dear Marcos, > > > > Thanks a lot for your answer and for offering me your help. From: Gianluca Interlandi (gianluca_at_u. Best, Jerome Le mardi 3 octobre 2006 01:01, Gianluca Interlandi a écrit :Reply: Gianluca Interlandi: "Re: Help building a desktop for namd" Messages sorted by: [ attachment ] On Mon, Apr 11, 2011 at 3:41 PM, Gianluca Interlandi <gianluca_at_u. There have been over 180 downloadsGianluca Interlandi, Wendy Thomas, The catch bond mechanism between von Willebrand factor and platelet surface receptors investigated by molecular dynamics simulations, "Proteins: Structure, Function, and Bioinformatics",. washington. On Thu, Apr 09, 2015 at 03:39:49PM -0700, Gianluca Interlandi wrote: > Dear list, > > Starting with version 1. From: Gianluca Interlandi (gianluca_at_u. > On Thu, Dec 2, 2010 at 2:35 PM, Gianluca Interlandi <gianluca_at_u. Sunhwan On Jul 16, 2014, at 12:32 AM, Gianluca Interlandi <gianluca_at_u. uiuc. uiuc. > > On Thu, Jul 12, 2012 at 3:21 PM, Gianluca Interlandi > <gianluca_at_u. From: Gianluca Interlandi (gianluca_at_u. edu) Date: Mon Apr 11 2011 - 16:21:27 CDT Next message: Gianluca Interlandi: "Re: Help building a desktop for namd" Previous message: Axel Kohlmeyer: "Re: Help building a desktop for namd" In reply to: Axel Kohlmeyer: "Re:. The Netherlands) is an antibody raised against K12 FimH-lectin domain (residues 1–160) and previously determined to recognize or induce the high affinity state of K12 FimH, especially in the presence of ligand ( buffer in wells of 96-well flat-bottom plates at 37 °C for 1 h. In reply to: Gianluca Interlandi: "Re: Force field design" Next in thread: Axel Kohlmeyer: "Re: Force field design" Reply: Axel Kohlmeyer: "Re: Force field design" Messages sorted by: [ attachment ] On 24 July 2014 22:22, Gianluca Interlandi <gianluca_at_u. edu) Date: Thu Apr 05 2012 - 17:04:15 CDT Next message: Gianluca Interlandi: "multicore versus net-linux" Previous message: Gianluca Interlandi: "RE: DCD" In reply to: Gianluca Interlandi: "RE: DCD" Next in thread: Buddhadev Maiti: "RE: DCD"Gianluca Interlandi Foege N430E gianluca_at_uw_dot_edu. The other> Auftrag von Gianluca Interlandi > Gesendet: Sonntag, 27. at 298. . Gianluca Interlandi 1 , Minhua Ling, An Yue Tu, Dominic W Chung, Wendy E Thomas Affiliation 1 Department of Bioengineering, University of Washington, Seattle, Washington, United States of America. FimH consists of a pilin domain (PD) that anchors it to the rest of the fimbria and an allosterically regulated le. Stenkamp, 3 Wendy E. 7 released" Messages sorted by: [ attachment ] Hi all, I pushed 2. edu> wrote: >>> if you want to go low risk and don't have much experience with GPU, then >>> probably the best deal you can currently get for running NAMD on small> 2011/6/29 Gianluca Interlandi <gianluca_at_u. Facilities. 7 with the PLUMED patch" In reply to: Gianluca Interlandi: "Compiling NAMD 2. e. edu) Date: Thu Jun 15 2006 - 21:01:04 CDT Next message: Taeho Kim: "free energy calculate" Previous message: L. edu) Date: Thu Nov 02 2006 - 13:55:24 CST Next message: Ugur Akgun: "ABF on a single molecule" Previous message: Al-Rawi, Ahlam: "external force" In reply to: Al-Rawi, Ahlam: "external force" Next in thread: Gianluca Interlandi:. View Gianluca Interlandi’s profile on LinkedIn, the world’s largest professional community. This school has it's > own biophysics division. washington. 3 hours/ns (stepsize 1, fullElectFrequency 1 and stepspercycle 20). On Thu, Jul 12, 2012 at 3:21 PM, Gianluca Interlandi < gianluca_at_u. It's > slightly faster but still not that much faster than running on 16 CPU cores. edu) Date: Thu Jun 15 2006 - 21:01:04 CDT Next message: Taeho Kim: "free energy calculate" From: Gianluca Interlandi (gianluca_at_u. The energy term mustOn Mon, 11 Apr 2011, Gianluca Interlandi wrote: > Salvador, > > You might also want to apply for computing time at one of the national > supercomputing centers through Teragrid. You should simulate it in explicit water (or try one of the implicitOn Tue, 14 Dec 2004, Gianluca Interlandi wrote: > Dear NAMD users, > > I have two independent questions: > > 1) Are there any experiences about the scalability running NAMD on > infiniband? I have been running NAMD on myrinet and, as an example, for > a system with 51000 atoms I get a seedup of 14 on 16 CPUs (dual opteron > 1800+). edu) Date: Thu Nov 02 2006 - 21:27:41 CST Next message: Dhiraj Srivastava: "production in NVE ensemble after equilibration in NPT ensemble" Previous message: Gianluca Interlandi: "Re: SMD on center of mass" In reply to: Gianluca Interlandi: "Re: SMD on center of mass"Re: Abe versus Lincoln. You should simulate it in explicit water (or try one of the implicitGianluca Interlandi is on Facebook. MyOne Bedroom Apartment, Sleeps 3 - C$150 avg/night - Ortigia - Amenities include: Internet, Air conditioning, TV, Satellite or cable, No smoking Bedrooms: 1 Sleeps: 3 Minimum 2 night(s) stay Bookable directly online - Book vacation rental 11131246 with Vrbo. washington. washington. washington. 7b1 on NCSA Abe. washington. Whitfield, 2 Esther Bullitt, 4 Ronald E. What can be the possible cause for this or does it happens naturally> On Tue, Aug 7, 2012 at 4:16 PM, Gianluca Interlandi <gianluca_at_u. " Previous message: Gianluca Interlandi: "multicore vs ibverbs" Messages sorted by: [ attachment ] Dear NAMD list, I am a bit. washington. edu) Date: Fri Jul 13 2012 - 14:08:57 CDT Next message: Dr. You simply load your trajectory > into VMD Reply: Gianluca Interlandi: "Re: Running NAMD on Forge (CUDA)" Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ] So your speed for 1 or 2 GPUs (based on what your sent) is about 1. From: Gianluca Interlandi (gianluca_at_u. washington. Interlandi et al. The simulations were not performed at constant velocity > but at constant force. Next in thread: Gianluca Interlandi: "Re: Should you cap C and N termini?" Reply: Gianluca Interlandi: "Re: Should you cap C and N termini?" Messages sorted by: [ attachment ] We generally use caps because our systems are individual domains within larger proteins. edu) Date: Thu Apr 09 2015 - 17:39:49 CDT Next message: Gianluca Interlandi: "Re: measure sasa not consistent" Previous message: John Stone: "Re: measure sasa not consistent" Next in thread: Gianluca Interlandi: "Re: measure energy"> From: Gianluca Interlandi [gianluca_at_u. edu] Sent: Friday, June 17, 2016 2:29 PM To: Richard Wood Cc: John Stone; vmd-l_at_ks. edu> wrote: > Hi! > > Are there any benchmarks available which compare the performance of NAMD on > Lincoln (CUDA heterogenous cluster) with its performance on a traditional > CPU only cluster like Abe? >Re: editing the code of the non bonded pair potentials. edu Subject: Re: namd-l: DCD Load your psf+dcd into VMD. gianluca@u. > > On Thu, Jul 12, 2012 at 3:21 PM, Gianluca Interlandi <gianluca_at_u. upenn. edu> wrote: > I would like to calculate the free energy of a protein-protein complex > using the Jarzinsky's equation from already performed SMD simulations. edu, Tel: (206) 685 4435, Fax: (206) 685 3300 1. " >> Could a small damping coefficient lead to such errors? If so, what would >> be the scenarioGianluca On Sun, 30 Aug 2009, Axel Kohlmeyer wrote: > On Sun, 2009-08-30 at 12:11 -0700, Gianluca Interlandi wrote: >> Thank you Mike for sharing your information. AMBER does, and so does GROMACS. 7 released" Reply: Gianluca Interlandi: "Re: NAMD 2. washington. Re: How to unsubscribe ? From: Gianluca Interlandi (gianluca_at_u. phone: 206 685 4435; office: N430E Foege Hall (Bioengineering) homepage: New UW Bioengineering research assistant professor Gianluca Interlandi studies the molecular function of blood proteins involved in hemostasis and clotting. com) Date: Wed Aug 27 2014 - 22:13:06 CDT Next message: Gianluca Interlandi: "Re:" Previous message: Douglas Houston: "Re: AW: Using nodelist file causes namd to hang" Next in thread: Gianluca Interlandi: "Re:" Reply: Gianluca Interlandi: "Re:" Messages sorted by: [. edu> > I suspect that E3_19 might not be stable with this type of implicit solvent > model (it doesn't contain a term to take the non-polar solvation energy into > accout). I am > using the option "wrapAll on". 5923 Kcal/mol also we have 6. View the profiles of professionals named "Gianluca Interlandi" on LinkedIn. > > > > I have already run a bunch of pulling simulations in the NVE ensemble. At the point of breaking the temperature raises of a few> Auftrag von Gianluca Interlandi > Gesendet: Sonntag, 27. edu> wrote: > With multicore I get 96 sec per 1000 steps from the Benchmark time. washington. uiuc. washington. washington. edu> wrote: >>> if you want to go low risk and don't have much experience with GPU, then >>> probably the best deal you can currently get for running NAMD on smallYesterday at about 11:45 a. -michael On Jun 15, 2006, at 5:31 PM, Gianluca Interlandi wrote:> 2011/6/29 Gianluca Interlandi <gianluca_at_u. Sarah Keller Professor. 1. edu> wrote: > What are your simulation parameters: >> >> timestep (and also any multistepping values) >> > 2 fs, SHAKE, no multistepping > > > cutoff (and also the pairlist and PME grid spacing) >> > 8-10-12 PME grid spacing ~ 1 A > > Interlandi G. In reply to: Gianluca Interlandi: "Re: Vibrational mode analysis" Next in thread: Gianluca Interlandi: "Re: Vibrational mode analysis" Reply: Gianluca Interlandi: "Re: Vibrational mode analysis" Messages sorted by: [ attachment ] Hi Gianluca, Unfortunately I don't know from where you can get such tutorials. Skip to search form Skip to main content Skip to account menu. From: Axel Kohlmeyer (akohlmey_at_gmail. washington. > > NCSA Forge has for example 6 CUDA devices and 16 CPU cores per node. Managing Member/Principal Atlantic Mortgage Partners, LLC Jun 2009 - Jun 2012 3 years 1. edu) Date: Thu Apr 07 2011 - 16:55:51 CDT Next message: THANH NGUYEN: "SMD simulation: stop applying force during simulation?" Previous message: johan strumpfer: "Re: Abe versus Lincoln" In reply to: johan strumpfer: "Re:. Gianluca, Yes, I think that a higher damping constant will indeed slow down conformational sampling. washington. 7b1)" Previous message: Christopher Hartshorn: "Re: FEP tutorial graph question" In reply to: Peter Freddolino:. From: Gianluca Interlandi (gianluca_at_u. edu> wrote:Gianluca Interlandi. washington. washington. From: Gianluca Interlandi (gianluca_at_u. washington.