> You could build a PC with the Asus p5Q Pro Motherboard, Intel Quadcore Q8200 > and two GTX 285 cards for under 900$ (plus the cost of the usual PC > components). You should simulate it in explicit water (or try one of the implicitRe: Protein in/out of box. 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. Just source the Tcl file and use the 'unwrap' procedure. 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. At some point there will be a web page here. Sunhwan On Jul 16, 2014, at 12:32 AM, Gianluca Interlandi <gianluca_at_u. > > NCSA Forge has for example 6 CUDA devices and 16 CPU cores per node. > > 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. Biochemistry. edu) Date: Wed Sep 23 2015 - 13:37:27 CDT Next message: Gianluca Interlandi: "SSD vs SSHD vs mechanical" Previous message: Mayne, Christopher G: "Re: FFTK Bond optimization" In reply to: Gianluca Interlandi: "SSD vs SSHD vs mechanical" Next in thread: Gianluca Interlandi: "Re:. washington. edu> wrote: >> Hi! >> >> Are there any benchmarks available which compare the performance of NAMD on >> Lincoln (CUDA heterogenous cluster) with its performance on a traditionalVMD-L Mailing List. Department of Bioengineering, University of Washington, Seattle, Washington, 98195. washington. Is it still possible to apply Jarzinsky's equation? > Also, according to your publication I have to integrate the work done along the. From: Gianluca Interlandi (gianluca_at_u. Search for: Main Menu. 6 ns/day for a 100k atom system with roughly those same parameters (and. 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. From: Gianluca Interlandi (gianluca_at_u. 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:. > > 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. 6 ns/day for a 100k atom system with roughly those same parameters (and. washington. It's > slightly faster but still not that much faster than running on 16 CPU cores. FimH. Gianluca has 2 jobs listed on their profile. edu) Date: Thu Apr 07 2011 - 13:57:41 CDT Next message: Axel Kohlmeyer: "Re: Abe versus Lincoln" Previous message: Gianluca Interlandi: "Re: Abe versus Lincoln" In reply to: Axel Kohlmeyer: "Re: Abe versus Lincoln"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. edu) Date: Fri May 04 2007 - 17:53:42 CDT Next message: Lechuga, Javier: "Simulating air with NAMD" Previous message: Gianluca Interlandi: "Re: query about wrapped coordinates" Maybe in reply to: Gianluca Interlandi: "Re: query about wrapped coordinates"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. Display options. 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. Sokurenko 1 , *. From: Gianluca Interlandi (gianluca_at_u. Electrical Engineering. 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:. . Just source the Tcl file and use the 'unwrap' procedure. Gianluca Interlandi, Department of Bioengineering, University of Washington, Box 355061, 3720 15th Ave NE, Seattle, WA 98195-5061, USA. The only significant change since 2. 7 released" Messages sorted by: [ attachment ] Dear Jim, Do you happen to have the. I needed to install the 'patch' program. edu) Date: Thu Jan 06 2011 - 16:55:03 CST Next message: Gianluca Interlandi: "Re: Compiling NAMD 2. edu) Date: Sat Apr 25 2009 - 12:05:17 CDT Next message: Gianluca Interlandi: "NAMD 2. AMBER does, and so does GROMACS. edu) Date: Thu Apr 07 2011 - 13:57:41 CDT Next message: Axel Kohlmeyer: "Re: Abe versus Lincoln" Previous message: Gianluca Interlandi: "Re: Abe versus Lincoln" In reply to: Axel Kohlmeyer: "Re: Abe versus Lincoln"Previous message: Gianluca Interlandi: "Re: Running NAMD on Forge (CUDA)" In reply to: Aron Broom: "Re: Am I doing the Right Thing?" Next in thread: Aron Broom: "Re: Am I doing the Right Thing?" Reply: Aron Broom: "Re: Am I doing the Right Thing?" Messages sorted by: [ attachment ] Hi Aron, I understand now what you are. unam. 7 released" Messages sorted by: [ attachment ] Thank you very much! It seems to be up to 40% faster than the 2. edu> wrote:Gianluca Interlandi. 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. edu> > wrote: > Roy, > > I think that you are confusing two things. Gianluca Interlandi, ‡, 1, 2 Olga Yakovenko, ‡, 1 An-Yue Tu,. Re: query about wrapped coordinates. 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. > 2011/6/29 Gianluca Interlandi <gianluca_at_u. 6 version, although I am not running the cluster at full load yet. Barry Lutz starts tenure-track position, Gianluca Interlandi joins faculty and Suzie Pun is promoted to full professor UW Bioengineering is pleased to announce the. Write a review. 7b1 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 overallIn reply to: Gianluca Interlandi: "Compiling NAMD 2. , and Thomas W. washington. Michel Espinoza-Fonseca: "Re: Vibrational. -Fatemeh On Fri, Dec 3, 2010 at 2:08 PM, Gianluca Interlandi < gianluca_at_u. Choose File -> Save Coordinates. uiuc. 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 smallOn Wed, 16 Sep 2020 at 11:40, Gianluca Interlandi <gianluca_at_u. The only significant change since 2. washington. edu> wrote: > With multicore I get 96 sec per 1000 steps from the Benchmark time. Gianluca Interlandi. From: Gianluca Interlandi (gianluca_at_u. edu> wrote: > Hi, > > I have a question concerning running NAMD on a CUDA cluster. 7 with the PLUMED patch" Messages sorted by: [ attachment ] Hi Gianluca, My guess is that something went wrong while patching namd with plumed. washington. You should simulate it in explicit water (or try one of the implicit From: Gianluca Interlandi <gianluca_at_u. Just a good MD toy ! Victor owner-namd-l_at_ks. washington. 26588. edu > Subject: Re: namd-l: DCD > > Load your psf+dcd into VMD. It's > slightly faster but still not that much faster than running on 16 CPU cores. Re: Vibrational mode analysis. But not now. Interlandi G. Is it appropriate to use a > >thermostat and barostat (CPT) while performing a constant force orRe: Force field design. washington. 7 ns/day, which seems decent given the system size. 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. At the point of breaking the temperature raises of a few> Auftrag von Gianluca Interlandi > Gesendet: Sonntag, 27. 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. washington. washington. > Le 2015-07-16 17:20, Gianluca Interlandi a écrit : >> Also, apropos documentation. edu > Subject: Re: namd-l: DCD > > Load your psf+dcd into VMD. 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 smallOn Thu, Jul 12, 2012 at 3:53 PM, Gianluca Interlandi < gianluca_at_u. VMD-L Mailing List. VMD-L Mailing List. 7 released" Messages sorted by: [ attachment ] Thank you very much! It seems to be up to 40% faster than the 2. washington. I am > using the option "wrapAll on". 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:. washington. 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",. Just a good MD toy ! Victor owner-namd-l_at_ks. Thanks for the reply. From: Gianluca Interlandi (gianluca_at_u. From: Gianluca Interlandi (gianluca_at_u. Re: Help building a desktop for namd. The simulations were not performed at constant velocity > but at constant force. NAMD doesn't that i know of. Gianluca Interlandi Research Assistant Professor. > > On Thu, Jul 12, 2012 at 3:21 PM, Gianluca Interlandi <gianluca_at_u. > > On Thu, Jul 12, 2012 at 3:21 PM, Gianluca Interlandi > <gianluca_at_u. washington. txt". washington. Re: Abe versus Lincoln. 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 smallmargin errors. Facebook gives people the power to share and makes the world more open and connected. > > Gianluca >Gianluca On Thu, 12 Jul 2012, Aron Broom wrote: > have you tried the multicore build? I wonder if the prebuilt smp one is just not > working for you. Re: Langevin process in NAMD tutorial" Previous message: Basak Isin: "Re: Regarding answering questions in a forum. Don't take my word that this works. Anderson: "Re: rlwrap problem on" In reply to: Frank Barry: "rlwrap problem on" Next in thread: Gianluca Interlandi: "Re: rlwrap problem on" Reply:. Michel Espinoza-Fonseca: "Re: Vibrational mode analysis" In reply to: L. From: Gianluca Interlandi (gianluca_at_u. 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. uiuc. edu) Date: Tue Jul 15 2014 - 22:32:35 CDT Next message: Gianluca Interlandi: "RE: Force field design" Previous message: Aron Broom: "Re: Force field design" In reply to: Abhishek TYAGI: "Force field design" Next in thread: Mayne,. 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. " >> 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. From: Axel Kohlmeyer (akohlmey_at_gmail. washington. 6 version, although I am not running the cluster at full load yet. washington. 7 with the PLUMED patch" Messages sorted by: [ attachment ] I found the problem. I > would be happy if somebody could point me out to some scripts which help me > perform that. The more tasks you have the > more frequently the CPUs need to update each other. Bioengineering. Is it still possible to apply Jarzinsky's equation? > Also, according to your publication I have to integrate the work done along the. Jennifer KongRE: DCD. 6 version, although I am not running the cluster at full load yet. washington. > > According to your banchmarks, it looks like the less expensive GTX285. E-mail: [email protected],. 0 and 2. edu) Date: Fri Jul 13 2012 - 14:08:57 CDT Next message: Dr. edu> wrote: >> blades generally tend to be a bit slower than "normal" nodes. > > 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):. 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,. Oktober 2013 07:12 > An: Roy Fernando > Cc: Axel Kohlmeyer; namd-l_at_ks. 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. 7b1 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 overallRe: Help building a desktop for namd. Thomas, 2 , * and Evgeni V. washington. MyOn Wed, Dec 1, 2010 at 1:54 AM, Gianluca Interlandi < gianluca_at_u. 7 out the door on Friday. You should simulate it in explicit water (or try one of the implicitGianluca Interlandi is on Facebook. Gianluca Interlandi, research assistant professor, and Wendy Thomas, professor: Antibody Dependent Enhancement, a type of immune system backfiring that causes increased infection in cells, is likely responsible for disappointing results on experimental vaccines for SARS and MERS, and. edu> wrote:Next in thread: Gianluca Interlandi: "Re: Infiniband and PME gridsize" Reply: Gianluca Interlandi: "Re: Infiniband and PME gridsize" Messages sorted by: [ attachment ] I don't think we have ever run NAMD on infiniband. 5923 Kcal/mol also we have 6. From: Gianluca Interlandi (gianluca_at_u. 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: [. washington. , "not (water or ions)" GianlucaRe: DCD. Next in thread: Gianluca Interlandi: "Re: NAMD 2. Reply: Gianluca Interlandi: "Re: Abe versus Lincoln" Messages sorted by: [ attachment ] Hi Gianluca, Using 4 Lincoln nodes with a 112580 atoms system I get 9. edu> wrote: > Roy, > > I think that you are confusing two things. edu) Date: Thu Apr 05 2012 - 17:04:15 CDT Next message: Gianluca Interlandi: "multicore versus net-linux" From: Gianluca Interlandi (gianluca_at_u. Facilities. 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:. washington. Interlandi Mortgage Consultants, LLC Dec 2008 - Present 14 years 3 months. edu on behalf of Gianluca Interlandi [gianluca_at_u. washington. Michel Espinoza-Fonseca: "Re: Vibrational. washington. Previous message: Gianluca Interlandi: "NAMD 2. On Tue, 19 Oct 2010, Gianluca Interlandi wrote: > Hi Jim, > > This is great! Is there also a compiled version for Clustermatic 5? > > Thanks, > > Gianluca > > On Tue, 19 Oct 2010, Jim Phillips wrote: > >> Hi all, >> >> I pushed 2. I > > attach a plot of a constant velocity simulation where I'm pulling two > > proteins apart. , "not. There have been over 180 downloadsReply: Gianluca Interlandi: "Re: Abe versus Lincoln" Messages sorted by: [ attachment ] Hi Gianluca, Using 4 Lincoln nodes with a 112580 atoms system I get 9. edu> wrote: > With multicore I get 96 sec per 1000 steps from the Benchmark time. Corresponding Author:gianluca@u. washington. Comparative controls consisted of FocH (high affinity with and. Email:. In the text field you can enter your atom selection, e. 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. Cancellation policy. washington. washington. Join Facebook to connect with Gianluca Interlandi and others you may know. From: Gianluca Interlandi (gianluca_at_u. washington. SASA in NAMD is used > internally to perform simulations in implicit solvent, whereas SASA in > VMD is used to analyse trajectories. 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: 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: Maxime Boissonneault: "Re: namd ibverbs" 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. Cheers! If you are looking for Virtual General Counsel, please go to: out professional insights posted by Isabella Interlandi, Attorney at Law, Legal adviser, UNSC 1540 Committee former Expert, Customs legislation and procedures. Abstract. Deadline is this Friday (or in three > months). 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. I have a new computer that came with Windows 10, which uses UEFI with a disk that has a GPT label. Academic ProgramsFrom: Gianluca Interlandi (gianluca_at_u. washington. edu> wrote: In reply to: Gianluca Interlandi: "Compiling NAMD 2. Does Berendsen increase viscosity of water? From: Gianluca Interlandi (gianluca_at_u. Does it also take account of the Urey-Bradley term? Many thanks, Gianluca ----- Gianluca Interlandi gianluca_at_bioc. On 6 May 2009, at 11:04, Gianluca Interlandi wrote: > Thanks Anton for your answer. Previous studies. washington. 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). Bathrooms: 1. washington. On Wed, Sep 23, 2015 at 02:28:07PM -0700, Gianluca Interlandi wrote: > The other question in the decision SSD vs HDD is the price tag. >Re: Vibrational mode analysis. Neil King Assistant Professor. > > On Thu, Jul 12, 2012 at 3:21 PM, Gianluca Interlandi > <gianluca_at_u. Chemistry. Re: Langevin process in NAMD tutorial"Gianluca On Mon, 11 Apr 2011, Axel Kohlmeyer wrote: > On Mon, Apr 11, 2011 at 3:41 PM, Gianluca Interlandi > <gianluca_at_u. 3 hours/ns (stepsize 1, fullElectFrequency 1 and stepspercycle 20). 7b1)" Previous message: Christopher Hartshorn: "Re: FEP tutorial graph question" In reply to: Peter Freddolino:. Balcony. washington. From: Gianluca Interlandi (gianluca_at_u. From: Gianluca Interlandi (gianluca_at_u. > > On Thu, Jul 12, 2012 at 3:21 PM, Gianluca Interlandi <gianluca_at_u. 7b4 is that> On Feb 8, 2007, at 11:49 PM, Gianluca Interlandi wrote: > > >I have a question concerning steered molecular dynamics simulations > >(constant force and constant velocity). 7 with the PLUMED patch" Messages sorted by: [ attachment ] I found the problem. I needed to install the 'patch' program. Gianluca > Gianluca > > On Thu, 12 Jul 2012, Aron Broom wrote: > > have you tried the multicore build? I wonder if the prebuilt > smp one is just not > working for you. washington. " Messages sorted by: [ attachment ] On Sun, 2009-08-30 at 12:11 -0700, Gianluca Interlandi wrote: > Thank you Mike for sharing your information. Previous message: Gianluca Interlandi: "Re: tools for Charmm" In reply to: Gianluca Interlandi: "Re: Charmm" Messages sorted by: [ attachment ] On 02/20/2014 01:10 PM, Gianluca Interlandi wrote: > I usually use the CHARMM program itself to generate a CHARMM PSF file. Gianluca Interlandi Foege N430E gianluca_at_uw_dot_edu My laboratory combines tools from computational structural biology, like molecular dynamics simulations and Monte Carlo methods, with biochemical and biophysical assays to unravel the molecular basis behind biological processes like the blood coagulation cascade and cellular adhesion. 15 K 1 KT = 2. From: Gianluca Interlandi [gianluca_at_u. at 298. Gianluca On Mon, 11 Apr 2011, Axel Kohlmeyer wrote: > On Mon, Apr 11, 2011 at 3:41 PM, Gianluca Interlandi > <gianluca_at_u. washington. >Gianluca Interlandi (Property Manager Baroque Apartments) Hosting since October 2020. washington. > On Thu, Dec 2, 2010 at 2:35 PM, Gianluca Interlandi <gianluca_at_u. I would be > happy if somebody could point me out to some scripts which help me performRe: checkpoint software for NAMD? From: 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. Re: Does Berendsen increase viscosity of water? From: Gianluca Interlandi (gianluca_at_u. 7 released" Reply: Gianluca Interlandi: "Re: NAMD 2. 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. Re: NAMD 2. E-mail: [email protected] > Betreff: Re: namd-l: Mysterious slow down in parallel > > You should read about domain decomposition. Re: Help building a desktop for namd. washington. washington. From: Mitchell Gleed (aliigleed16_at_gmail. 3 hours/ns (stepsize 1, fullElectFrequency 1 and stepspercycle 20). washington. Proteins 78, 2506–2522 [PMC free article] [Google Scholar]Previous message: Gianluca Interlandi: "Re: Compiling NAMD 2. Electrical. 3 hours/ns (stepsize 1, fullElectFrequency 1 and stepspercycle 20). Hope the video helps, but now I'm embarrassed. View all 11 amenities. 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:. Re: Abe versus Lincoln. edu) Date: Wed Aug 05 2009 - 13:19:25 CDT Next message: Gianluca Interlandi: "Re: SMD output : which col represents force, second or last" Previous message: David Tanner: "Re: SMD output : which col represents force, second or last" In. I would be > happy if somebody could point me out to some scripts which help me perform(no subject) From: BIPLAB NANDI (dafodils2002_at_gmail. SASA in NAMD is used internally > to perform simulations in implicit solvent, whereas SASA in VMD is used to > analyse trajectories. edu> wrote: > With multicore I get 96 sec per 1000 steps from the Benchmark time. washington. washington. (did you see if any hunk failed?) Gianluca > Gianluca > > On Thu, 12 Jul 2012, Aron Broom wrote: > > have you tried the multicore build? I wonder if the prebuilt > smp one is just not > working for you. washington. washington. > > Gianluca > > > On Thu, 12 Jul 2012, Aron Broom wrote: > > have you tried the multicore build?On Tue, Aug 7, 2012 at 4:16 PM, Gianluca Interlandi < gianluca_at_u. washington. 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. This is unrelated to KDE3. washington. washington. 7b1 on NCSA Abe. Jessica is a seasoned litigator, having graduated from the. New UW Bioengineering research assistant professor Gianluca Interlandi studies the molecular function of blood proteins involved in hemostasis and clotting. Whitfield, 2 Esther Bullitt, 4 Ronald E. Reply: Gianluca Interlandi: "Re: Changing Boundary conditions from PBC to non-periodic" Messages sorted by: [ attachment ] Dear NAMD users, A portion of my protein is outside of the simulation box. edu Subject: RE: vmd-l: Can't read DCD files generated using NAMD. washington. uiuc. 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. I doubt that there is a way to have> On Thu, Apr 7, 2011 at 2:22 PM, Gianluca Interlandi > <gianluca_at_u. > On Wed, Dec 1, 2010 at 1:54 AM, Gianluca Interlandi <gianluca_at_u. Usually, this > is > written in the dcd file if you specified "DCDUnitCell yes" in your > NAMD > config file. washington. washington. > However, topology and parameters for water and ions are. Search 214,979,228 papers from all fields of science. 7 released" Reply: Gianluca Interlandi: "Re: NAMD 2. washington. washington. Proteins 78, 2506–2522 [PMC free article] [Google Scholar] > On Wed, 16 Sep 2020 at 11:40, Gianluca Interlandi <gianluca_at_u. 7 released. On Thu, Jul 12, 2012 at 3:21 PM, Gianluca Interlandi < gianluca_at_u. Both > simulations were started from X-ray structures. washington. 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:. From: Gianluca Interlandi (gianluca_at_u. edu) Date: Fri May 01 2009 - 12:18:05 CDT Next message: Grace Brannigan: "Re: crash with more than 96 processors (v2. washington. Search for: Main Menu Author Summary A common approach in the development of selective inhibitors for ligand-receptor interactions is targeting the receptor binding site with the expectation that inhibitors will sterically interfere with ligand binding and thus block receptor function via a competitive (orthosteric) mechanism. On Thu, Apr 7, 2011 at 2:22 PM, Gianluca Interlandi <gianluca_at_u. washington. washington. , and Thomas W. washington. 0 and 2. Check the NAMD log! Any errors or warnings?"wrapAll on" with a complex. washington. 26055 Abstract The blood protein von Willebrand factor (VWF) is a key link between inflammation and pathological thrombus formation. washington. Oktober 2013 07:12 > An: Roy Fernando > Cc: Axel Kohlmeyer; namd-l_at_ks. at 298. washington. I know this can be just a detail, but it is quite tricky. PMID: 37700555; DOI: 10. Re: Yet another NAMD speed concerns. , Thomas W. 7 with the PLUMED patch" Messages sorted by: [ attachment ] I found the problem. 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)" Complex between VWF A1 and GpIbα and amino acid sequence of the A1 domain. 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 NAMD output theFrom: Gianluca Interlandi (gianluca_at_u. edu> > wrote:From: Gianluca Interlandi [gianluca_at_u. washington. washington. washington. It is experimentally knownReply: 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. I was recording the energies once every 100 steps. Gianluca From: Gianluca Interlandi (gianluca_at_u. washington. 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. The simulations were not performed at constant velocity > but at constant force. Michel Espinoza-Fonseca: "Re: Vibrational. 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 ] kcal/mol/A^2 is actually units for a force constant (for a spring for. 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. I’m working in Research Assistant Professor Gianluca Interlandi’s research lab, and I study the behavior of the Von Willebrand factor (VWF), which is a plasma protein that recruits platelets to the site of blood vessel injury. It's > slightly faster but still not that much faster than running on 16 CPU cores. 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. 85. Previous message: Gianluca Interlandi: "Re: Compiling NAMD 2. 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)" From: Gianluca Interlandi (gianluca_at_u. 7b1 on Abe" Previous message: Gianluca Interlandi: "Re: Yet another NAMD speed concerns" In reply to: Gianluca Interlandi: "Re: Yet another. 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.