[gmx-users] Re: gmx-users Digest, Vol 111, Issue 112

Dear Justin, Thanks for your answer... I move so far... My aim was to ask gromacs to read directly a modify protein SOL+NA, not protein SOL NA But I have not succeed so far. Best regards Collins On Wed, Jul 24, 2013 at 8:38 AM, wrote: > Send gmx-users mailing list submissions to >

[gmx-users] Re: Umbrella Sampling _ pulled ion

Think your .mdp-file looks reasonable. If you are totaly unsure you could determine the PMF of two water molecules. As a reference one can use the radial distribution function g(r) and calculate the PMF as V_pmf(r) = -kT LN(g(r)) One side note: Since the force constant you are using is relativ

Re: [gmx-users] Re: Limitations of simulations?

On 7/25/13 12:44 AM, Jonathan Saboury wrote: Hm, I am probably completely wrong about this, but can you do implicit solvent and Periodic Box Conditions? That's not typical. I suppose one could do an NVT simulation, but the only stable way I have found to run in implicit solvent is to use i

[gmx-users] Re: Limitations of simulations?

Hm, I am probably completely wrong about this, but can you do implicit solvent and Periodic Box Conditions? -- View this message in context: http://gromacs.5086.x6.nabble.com/Limitations-of-simulations-tp5010100p5010103.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com.

[gmx-users] Re: editconf: Invalid command line argument: –f

Yep, the pdf was not written or copy and pasted the "-" incorrectly. Thanks :) -Jonathan On Fri, Jul 12, 2013 at 3:03 PM, Jonathan Saboury wrote: > I am following "Tutorial 1" from > https://extras.csc.fi/chem/courses/gmx2007/tutorial1/index.html > > I try the command "editconf –f conf.gro –b

[gmx-users] Re: Simulating a semi-membrane protein

Thank you both of you for taking time to help me.. This would be definitely useful. thank you so much. -- View this message in context: http://gromacs.5086.x6.nabble.com/Simulating-a-semi-membrane-protein-tp5010032p5010063.html Sent from the GROMACS Users Forum mailing list archive at Nabble.

[gmx-users] Re: gmx-users Digest, Vol 111, Issue 101

Dear Justin, Thank you for your suggestion... Best regards Collins On Mon, Jul 22, 2013 at 10:00 AM, wrote: > Send gmx-users mailing list submissions to > gmx-users@gromacs.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.gromacs.org/mail

Re: [gmx-users] Re: Simulating a semi-membrane protein

Dear Pavithrakb, First of all, your choice will depend on the available parameters for the lipid molecules that you want to simulate (check the Lipidbook repository ). Concerning the GROMOS force fields the most recent lipid parameters are the ones included in th

Re: [gmx-users] Re: Simulating a semi-membrane protein

On 7/23/13 7:46 AM, pavithrakb wrote: Sir, I'm new to simulation. is there any papers or materials (book or website) to learn about the forcefields and their limitations. All the advice I get from people is to select a ff and membrane based on the previous works on that protein or protein famil

[gmx-users] Re: Simulating a semi-membrane protein

Sir, I'm new to simulation. is there any papers or materials (book or website) to learn about the forcefields and their limitations. All the advice I get from people is to select a ff and membrane based on the previous works on that protein or protein family. I know its too much to ask but, can you

Re: [gmx-users] Re: Simulating a semi-membrane protein

On 7/22/13 10:21 PM, pavithrakb wrote: Dear Sir, Thank you. I understand it now. But, when apply the force field, should I select the membrane ff like gromos56 (like in your KALP tutorial) or will it be a complex process to select a ff? Choosing a force field is always complicated. There ar

[gmx-users] Re: Simulating a semi-membrane protein

Dear Sir, Thank you. I understand it now. But, when apply the force field, should I select the membrane ff like gromos56 (like in your KALP tutorial) or will it be a complex process to select a ff? -- View this message in context: http://gromacs.5086.x6.nabble.com/Simulating-a-semi-membrane-pr

[gmx-users] Re: Simulating a semi-membrane protein

Dear Sir, Thank you. I understand it now. But, when apply the force field, should I select the membrane ff like gromos56 (like in your KALP tutorial) or will it be a complex process to select a ff? -- View this message in context: http://gromacs.5086.x6.nabble.com/Simulating-a-semi-membrane-pr

[gmx-users] Re: Problem with Amber99SB-ILDN ff

Hi, This is more or less that I was thinking after look carefully all the errors. Thank you for your answer and your time. Melchor S. -- View this message in context: http://gromacs.5086.x6.nabble.com/Problem-with-Amber99SB-ILDN-ff-tp5009641p5010029.html Sent from the GROMACS Users Forum ma

Re: [gmx-users] Re: Problem with Amber99SB-ILDN ff

Hi I can't see which commands you typed. Your second try "/bin/sh: 1: -i: not found" means that you $PATH is not properly setup for Amber Tools. And if you using open babel, it has to be your $PATH as well. For the first case, it's all about which structure you were trying to run. >From the pdbs

[gmx-users] Re: Question on Hessian and forces not being preserved on restart with Hessian calculation?

Problem partly addressed. If I run normal modes in -nt 1, then I get the same force as after the minimization. I'll file a redmine. On Sat, Jul 20, 2013 at 9:43 AM, Michael Shirts wrote: > To follow up -- if I try to minimize again using -t, I get the same > low forces as in the minimization in

[gmx-users] Re: Question on Hessian and forces not being preserved on restart with Hessian calculation?

To follow up -- if I try to minimize again using -t, I get the same low forces as in the minimization in the previous step. So it appears to be something with what do_nm is doing, not with errors in the output structure. On Sat, Jul 20, 2013 at 9:37 AM, Michael Shirts wrote: > When I minimize a

Re: [gmx-users] Re: gmx 4.6.1, Expanded ensemble: weird balancing factors

Unfortunately, the semiiso fix for MTTK is not trivial, and will have to wait until 5.0. Berendsen volume + expanded ensemble would likely give very bad results, especially since surface area fluctuations are important. Replica exchange works with sd and parrinello-Rahman, if that helps! I am wo

Re: [gmx-users] Re: gmx 4.6.1, Expanded ensemble: weird balancing factors

The test I did was using gmx-4.6.3. I'm currently working on a membrane system, which requires semiisotropic pressure coupling. I know that MTTK in gmx-4.6.3 doesn't support semiiso yet so the only combination available for expanded ensemble is md-vv + v-rescale tcoupl + berendsen pcoupl, which I'm

Re: [gmx-users] Re: gmx 4.6.1, Expanded ensemble: weird balancing factors

> It seems to have something to do with the integrator/pressure-coupling. that is what I expected based on some preliminary testing earlier. When > I ran the tutorial on > http://www.alchemistry.org/wiki/GROMACS_4.6_example:_Ethanol_solvation_with_expanded_ensemble, > everything seems fine OK go

Re: [gmx-users] Re: window exchange umbrella sampling

4.5.7 does not support Hamiltonian exchange. It says all properties are the same, because all the temperatures and pressures are the same -- it won't switch the umbrellas. On Wed, Jul 17, 2013 at 3:30 PM, Parisa wrote: > Hi Michael, > > I think that this is an issue with the gromacs version I am

[gmx-users] Re: window exchange umbrella sampling

Hi Michael, I think that this is an issue with the gromacs version I am using (4.6.1). I switched to 4.5.7 and now, I get the error: Fatal error: The properties of the ... systems are all the same, there is nothing to exchange I don't understand what I am missing here. I suppose if I have 3 repl

[gmx-users] Re: gmx 4.6.1, Expanded ensemble: weird balancing factors

It seems to have something to do with the integrator/pressure-coupling. When I ran the tutorial on http://www.alchemistry.org/wiki/GROMACS_4.6_example:_Ethanol_solvation_with_expanded_ensemble, everything seems fine unless I switched to sd integrator instead of md-vv (and Pcoupl from MTTK to beren

[gmx-users] Re: Problem with Amber99SB-ILDN ff

Hi again, I can give more details about acpype error. This is the error that I obtained, === | ACPYPE: AnteChamber PYthon Parser interfacE v. 2012-09-13 14:55:47Z Rev: 389 (c) 2012 AWSdS | =

Re: [gmx-users] Re: window exchange umbrella sampling

Ah, this is a force field issue -- urey-bradley terms are not supported free energy calculations. However, since only restraints are changing, this warning doesn't really need to be there. It would be relatively simple to put in a check to allow this to work, but it might take a week or two to get

[gmx-users] Re: window exchange umbrella sampling

Thanks for quick reply. I fixed the issue with kB1. Below is what I have changed in the .mdp file. I use this to run it "mpirun -np 3 mdrun_mpi -s prefix_.tpr -multi 3 -replex 6 -dhdl a.dhdl". But I get this error (I am using version 4.6.1): Fatal error: Function type U-B not implemented in ip_pe

Re: [gmx-users] Re: gmx 4.6.1, Expanded ensemble: weird balancing factors

That's a good question. My understanding and experience is the difference in required overlap in replica exchange and expanded ensemble methods is not significant. There are probably some more detailed studies out there. Expanded ensemble can be somewhat more efficient (see a paper by Park and Pa

Re: [gmx-users] Re: gmx 4.6.1, Expanded ensemble: weird balancing factors

Hi Michael, Thanks for the reply. Just a quick follow-up. Do you think the overlap of energy histogram between different lambdas matter for lambda-dynamics in general? (Maybe not in this particular case or in the case of the tutorial you just posted.) I wonder if we need as many intermediate lambd

Re: [gmx-users] Re: gmx 4.6.1, Expanded ensemble: weird balancing factors

Hi, all- This not a problem with W-L, but is instead something that is wrong with a particular combination of mdp options that are not working for expanded ensemble simulations. W-L can equilibrate to incorrect distributions because it decreases the weights too fast (more on that later), but that

[gmx-users] Re: gmx 4.6.1, Expanded ensemble: weird balancing factors

I have a similar question here. Can anyone tell if the Wang-Landau algorithm in lambda space is robust in that it doesn't depend on the choice of the convergence factor (weight-equil-wl-delta), the flatness of the histogram (wl-ratio) and/or the frequency of trial move (nstexpanded), especially in

[gmx-users] Re: Problem with energy minimization parameters

Hi Justin, Thanks for suggestion...and pointing out that there is problem with topology ...now i checked ligand file..there hydrogens were not added correctly..so swissparam tool was not correct topology .. now i corrected it ..it works perfectly .. Thanks a lot Sainitin On Tue, Jul 16, 2013 a

Re: [gmx-users] Re: extreme projections

Hi, If you have VMD installed, load the "extreme.pdb". Then in graphics> Representations--->Trajectory---> put values in "Draw Multiple Frames", for e.g. 0:10 this will show the extremes of 0th frame to 10th frame (you can change this a/c to your representation). After this selecting Draw sty

[gmx-users] Re: enery conserving problem in NVE simulations with SMW4-NPD polarizable force field

On Mon, Jul 15, 2013 at 3:00 AM, wrote: > Send gmx-users mailing list submissions to > gmx-users@gromacs.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.gromacs.org/mailman/listinfo/gmx-users > or, via email, send a message with subject or body 'he

Re: [gmx-users] RE: Is non-linear data output/storage possible?

On 7/15/13 11:48 AM, Neha wrote: Justin Lemkul wrote The .cpt file stores information related to output frequency. The existing.cpt file designates output every X steps, while the new .tpr file specifies output every Y steps, and X != Y, so mdrun complains. I'm assuming mdrun aborts at that

[gmx-users] RE: Is non-linear data output/storage possible?

Justin Lemkul wrote > The .cpt file stores information related to output frequency. The > existing.cpt > file designates output every X steps, while the new .tpr file specifies > output > every Y steps, and X != Y, so mdrun complains. I'm assuming mdrun aborts > at > that point? Have you tried w

Re: [gmx-users] Re: snapshot

Thanks *Thomas* --Rama On Mon, Jul 15, 2013 at 9:00 AM, Thomas Schlesier wrote: > Hi, > the following: > > trjconv -s md.tpr -f md.trr -o beta.gro -dt 250 -sep > > should work. > -dt 250 ; write output every 250 ps > -sep ; to write each frame (but the output frequency gets overwritten by >

[gmx-users] Re: snapshot

Hi, the following: trjconv -s md.tpr -f md.trr -o beta.gro -dt 250 -sep should work. -dt 250 ; write output every 250 ps -sep ; to write each frame (but the output frequency gets overwritten by '-dt 250') the additional use of '-dump x' might be the problem, since with '-dump x' GMX writes o

[gmx-users] Re: extreme projections

any one please help me out with this problem? 2013/7/10 Ahmet yıldırım > Dear users, > > I extracted separate extreme projections using g_anaeig. I have to make > pictures which show the difference. Can you help me, someone who makesthem > using pymolbefore > ? > > -- > Ahmet Yıldırım > --

Re: [gmx-users] Re: Umbrella Sampling settings

Friday, July 12, 2013 9:04 PM Subject: [gmx-users] Re: Umbrella Sampling settings In GROMACS groups are called via the *.ndx file (default: index.ndx) Be aware that 'pull_dim' determines in which diretions (x,y,z) the umbrella potential acts. So use N N Y , if you want that the ion can

Re: [gmx-users] Re: Umbrella Sampling settings

s" (Y). So what should I do?!   Sincerely, Shima - Original Message - From: Thomas Schlesier To: gmx-users@gromacs.org Cc: Sent: Friday, July 12, 2013 9:04 PM Subject: [gmx-users] Re: Umbrella Sampling settings In GROMACS groups are called via the *.ndx file (default: inde

[gmx-users] Re: Umbrella Sampling settings

In GROMACS groups are called via the *.ndx file (default: index.ndx) Be aware that 'pull_dim' determines in which diretions (x,y,z) the umbrella potential acts. So use N N Y , if you want that the ion can move freely (onsidering the pull) in the xy-plane and Y Y Y if you want to also restrit th

Re: [gmx-users] Re: DCD can not open file 'md_0_1.xtc' for reading

On 7/12/13 9:34 AM, maggin wrote: I use pdb to do test : catdcd -o 1dx0.gro 1dx0.pdb error: CatDCD 4.0 dcdplugin) unrecognized DCD header: dcdplugin) [0]: 1380273473 [1]: 538987346 dcdplugin) [0]: 0x52454d41 [1]: 0x20204b52 dcdplugin) read_dcdheader: corruption or unrecognized fi

[gmx-users] Re: DCD can not open file 'md_0_1.xtc' for reading

I use pdb to do test : catdcd -o 1dx0.gro 1dx0.pdb error: CatDCD 4.0 dcdplugin) unrecognized DCD header: dcdplugin) [0]: 1380273473 [1]: 538987346 dcdplugin) [0]: 0x52454d41 [1]: 0x20204b52 dcdplugin) read_dcdheader: corruption or unrecognized file structure Error: could not open file

[gmx-users] Re: DCD can not open file 'md_0_1.xtc' for reading

at redhat INUXAMD64 use: catdcd -o md_0_1.xyz md_0_1.xtc error: CatDCD 4.0 dcdplugin) unrecognized DCD header: dcdplugin) [0]: 1995 [1]: 1059782656 dcdplugin) [0]: 0x07cb [1]: 0x3f2b dcdplugin) read_dcdheader: corruption or unrecognized file structure Error: could not open

[gmx-users] Re: Umbrella Sampling settings

But you need each of these lines for both cases (SMD and US). Probably one could skip two lines and use the default values, but it's better to set them manually. See below for comments (comments are under the related entry): Thanks for your reply. But when I don't understand why these extra

Re: [gmx-users] RE: Is non-linear data output/storage possible?

On Thu, Jul 11, 2013 at 11:41 PM, Neha wrote: > > > The .cpt file stores information related to output frequency. The existing > .cpt > file designates output every X steps, while the new .tpr file specifies > output > every Y steps, and X != Y, so mdrun complains. I'm assuming mdrun aborts at >

Re: [gmx-users] RE: Is non-linear data output/storage possible?

On 7/11/13 6:41 PM, Neha wrote: The .cpt file stores information related to output frequency. The existing .cpt file designates output every X steps, while the new .tpr file specifies output every Y steps, and X != Y, so mdrun complains. I'm assuming mdrun aborts at that point? Have you tr

[gmx-users] RE: Is non-linear data output/storage possible?

The .cpt file stores information related to output frequency. The existing .cpt file designates output every X steps, while the new .tpr file specifies output every Y steps, and X != Y, so mdrun complains. I'm assuming mdrun aborts at that point? Have you tried with -noappend? Hi, So this

Re: [gmx-users] RE: Is non-linear data output/storage possible?

On 7/11/13 3:14 PM, Neha wrote: Hi everybody, I started changing init-step. Now I seem to have another problem. When I go to switch to another 'block' it tells me that my input and checkpoint states are not identical when I use mdrun the second time. I am not sure how they can be any different

[gmx-users] RE: Is non-linear data output/storage possible?

Hi everybody, I started changing init-step. Now I seem to have another problem. When I go to switch to another 'block' it tells me that my input and checkpoint states are not identical when I use mdrun the second time. I am not sure how they can be any different as I only have one .cpt file in the

Re: [gmx-users] Re: Atomtype OWT3 not found during EM step

On 7/11/13 11:47 AM, juganta wrote: Thanks Justin for your information. But I got those lines in /gromacs 4.5.5/top/tip3p.itp -- #ifdef _FF_GROMACS #include "gmx.ff/tip3p.itp" #endif #ifdef _FF_GROMOS96 #include "gromos43a1.ff/tip3p.itp" #endif #ifdef _FF_OPLS #include "oplsaa.ff/tip3p.itp" #e

[gmx-users] Re: Atomtype OWT3 not found during EM step

Thanks Justin for your information. But I got those lines in /gromacs 4.5.5/top/tip3p.itp -- #ifdef _FF_GROMACS #include "gmx.ff/tip3p.itp" #endif #ifdef _FF_GROMOS96 #include "gromos43a1.ff/tip3p.itp" #endif #ifdef _FF_OPLS #include "oplsaa.ff/tip3p.itp" #endif I thought I can use tip3p.itp wi

[gmx-users] Re: gmx-users Digest, Vol 111, Issue 53

Hi Trayder, Thank you for the suggestion. I will try the plugin soon. Yes, I can play the two trajectories simultaneously, one with protein disabled. In this way, I indeed can get a very good presentation of what is happening. However, it's quite inconvenient to set Graphical Representations in V

Re: [gmx-users] Re: gInstallation Problems with Gromacs4.6

I figured out by using static libraries. On 07/10/2013 06:52 AM, Éric Germaneau wrote: Dear all, I call cmake the following way and get the error bellow: CC=mpicc CXX=mpicxx CMAKE_PREFIX_PATH=$FFTW3DIR:$CUDAPATH/include:$CUDAPATH/lib64:$CUDAPATH/bin \ /lustre/utility/bin/cmake \ -D

[gmx-users] Re: Fatal error: No donor atom 780

Never mind, everyone. Issue solved by always selecting the smaller index group first. On Wed, Jul 10, 2013 at 10:59 AM, yunshi11 . wrote: > Program g_hbond, VERSION 4.5.4 > Source code file: gmx_hbond.c, line: 823 > > Fatal error: > No donor atom 5226 > > > > On Wed, Jul 10, 2013 at 10:58 AM, yu

[gmx-users] Re: Fatal error: No donor atom 780

Program g_hbond, VERSION 4.5.4 Source code file: gmx_hbond.c, line: 823 Fatal error: No donor atom 5226 On Wed, Jul 10, 2013 at 10:58 AM, yunshi11 . wrote: > Hi all, > > I wonder what could be the cause of such a fatal error when using g_hbond > with -contact option. > > The two index group I

RE: [gmx-users] Re: Re: Re: Re: Which/What is the adequate overlap

mpibpc.mpg.de www.bisb.uni-bayreuth.de/People/ullmannt -- From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Mike Nemec [mike.ne...@stud.uni-due.de] Sent: Wednesday, July 10, 2013 1:13 PM To: gmx-users@gromacs.org Subject:

[gmx-users] Re: Re: Re: Re: Which/What is the adequate overlap

Hi Thomas, thank you for your reply. Hi Mike, Your confusion might stem from a very simple issue. To see the overlap of the forward and backward distributions, you have to plot N(+Delta H(lambda=x) | lambda=y) and N(-Delta H(lambda=y) | lambda=x). Do I understand it right, that for instanc

Re: [gmx-users] Re: Problem with Amber99SB-ILDN ff

Hi there, You said ACPYPE didn't work… Can you give details? Have you try with GAFF first? If you don't mind, can you post me your molecule in private email? Thanks, Alan On 9 July 2013 22:34, Melchor S. wrote: > Sorry for the misunderstanding. I should had explained it better. > > I know th

Re: [gmx-users] Re: Multiple LINCS Warnings in NVT Equillibration

On 7/10/13 3:13 AM, ashish24294 wrote: I changed the cut-offs as follows, still isn't helping. I tried restraining the urea which also didn't work. I have attached the topology as well. topolurea.top The urea.itp looks suspicio

Re: [gmx-users] Re: Problem with Amber99SB-ILDN ff

On 7/9/13 5:34 PM, Melchor S. wrote: Sorry for the misunderstanding. I should had explained it better. I know that is a zwitterionic residue, I have run several simulations with the same PDB and with other forcefields. ACPYPE does not work, I tried it yesterday, but I have to check it. Antecha

[gmx-users] Re: Umbrella sampling- force vs time plots

Generally: Using a higher force constant and / or pulling velocity drives the system faster out of equilibrium, which results in higher rupture forces. Varying the force constant has two effects. The softer the potential is, the larger are the fluctuations in the coordinates but the lower are th

[gmx-users] Re: Multiple LINCS Warnings in NVT Equillibration

I changed the cut-offs as follows, still isn't helping. I tried restraining the urea which also didn't work. I have attached the topology as well. topolurea.top *The nvt.mdp* title = UREA_in_WATER NVT equillibration ;define

[gmx-users] Re: Multiple LINCS Warnings in NVT Equillibration

Thank you!! But it still didn't work!! -- View this message in context: http://gromacs.5086.x6.nabble.com/Multiple-LINCS-Warnings-in-NVT-Equillibration-tp5009701p5009722.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.or

[gmx-users] Re: gInstallation Problems with Gromacs4.6

Dear all, I call cmake the following way and get the error bellow: CC=mpicc CXX=mpicxx CMAKE_PREFIX_PATH=$FFTW3DIR:$CUDAPATH/include:$CUDAPATH/lib64:$CUDAPATH/bin \ /lustre/utility/bin/cmake \ -DCMAKE_CXX_COMPILER=/xxx/xxx/intel/impi/4.1.1.036/intel64/bin/mpicxx \ -DCMAKE_C_

[gmx-users] Re: Problem with Amber99SB-ILDN ff

Sorry for the misunderstanding. I should had explained it better. I know that is a zwitterionic residue, I have run several simulations with the same PDB and with other forcefields. ACPYPE does not work, I tried it yesterday, but I have to check it. Antechamber I don't know, I have to try it. Als

Re: [gmx-users] Re: Problem with Amber99SB-ILDN ff

On 7/9/13 11:23 AM, Melchor S. wrote: I am using gromacs 4.5.5, I didn't tell you yesterday. I have been tried a lot of things, but without any success. One of that I think has to work fine, is with the NGLU nomenclature, but when I use it, I obtain this There is a dangling bond at at least o

[gmx-users] Re: Problem with Amber99SB-ILDN ff

I am using gromacs 4.5.5, I didn't tell you yesterday. I have been tried a lot of things, but without any success. One of that I think has to work fine, is with the NGLU nomenclature, but when I use it, I obtain this There is a dangling bond at at least one of the terminal ends and the force fiel

RE: [gmx-users] Re: Re: Which/What is the adequate overlap using g_BAR

boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Mike Nemec [mike.ne...@stud.uni-due.de] Sent: Tuesday, July 09, 2013 4:01 PM To: gmx-users@gromacs.org Subject: [gmx-users] Re: Re: Which/What is the adequate overlap using g_BAR >> Dear Gromacs People, >> >> I

[gmx-users] Re: Re: Which/What is the adequate overlap using g_BAR

Dear Gromacs People, I want to calculate free energy differences between two states A and B using g_BAR. For this I read many papers concerning the overlap between neighboring sample windows (Delta H) but I am still wondering about the following issue: I know, that there has to be an adequa

[gmx-users] Re: g_cluster

hi, Justin I read the paper Daura(1999) and other papers: "Ensemble-based convergence analysis of biomolecular trajectories"(2006) "Helix propensities of short peptide: Molecular dynamics versus bioinformatics" (2003) "Assessing equilibration and convergence in biomolecular simulation" (2002) bu

Re: [gmx-users] Re: Atomtype OWT3 not found during EM step

On 7/8/13 1:08 PM, juganta wrote: Thanks Justin for your reply. What I actually did, I edited the .atp file by hand as follows- OWT3 15.99940 ; TIP3P WATER OXYGEN HW 1.00800 ; WATER HYDROGEN and I added those lines in the [atomtypes] section of ffnonbonded.itp file- OWT3

[gmx-users] RE: About Potential energy calculation

Hi, Won Ok, what I did was not exactly as is described. I attach the bash script that I made to do this I use the trajectory file to extract EACH frame and safe it in an independent file using trjconv . And when I do the extraction, I only extract the protein of interest, this can be done bec

[gmx-users] Re: Atomtype OWT3 not found during EM step

Thanks Dr. Chaban for your suggestion. I included atom type in itp file. But I have know idea how do I edited pairs or triples of atoms. Would you please help me how do I fix it? -- View this message in context: http://gromacs.5086.x6.nabble.com/Atomtype-OWT3-not-found-during-EM-step-tp500952

[gmx-users] Re: Atomtype OWT3 not found during EM step

Thanks Justin for your reply. What I actually did, I edited the .atp file by hand as follows- OWT3 15.99940 ; TIP3P WATER OXYGEN HW 1.00800 ; WATER HYDROGEN and I added those lines in the [atomtypes] section of ffnonbonded.itp file- OWT38 0.000 0.000 A 0.24889e-02

Re: [gmx-users] Re: problem in g_membed

Just a piece of advices: you can consider equilibrate a lipids system which is large enough for your protein. This will save you huge amount of time on using tricks to add water later or enlarge the lipids. The system MUST BE IN PBC BOX for the g_membed input coordinate, otherwise your job w

[gmx-users] Re: Problem with Amber99SB-ILDN ff

For sure there are a lot of variable playing here, I only ask about the MET for curiosity, because I am a beginner in this kind of things we can say... I do : pdb2gmx -f pdb.pdb -p pdb.top -o pdb.gro -water spc -his -ter -posrefc 1. I don't specify nothing as separate chains or so on. I wil

Re: [gmx-users] Re: Problem with Amber99SB-ILDN ff

On 7/8/13 7:00 AM, Melchor S. wrote: Ok, I will try it. Thank you. But when a chain starts with MET why this nomenclature is not needed? Because with MET works fine like any other forcefield. There are a lot of variables at play here that you haven't described (Gromacs version, pdb2gmx comm

[gmx-users] Re: Problem with Amber99SB-ILDN ff

Ok, I will try it. Thank you. But when a chain starts with MET why this nomenclature is not needed? Because with MET works fine like any other forcefield. -- View this message in context: http://gromacs.5086.x6.nabble.com/Problem-with-Amber99SB-ILDN-ff-tp5009641p5009643.html Sent from the GROMA

Re: [gmx-users] Re: problem in g_membed

On 7/7/13 10:52 PM, pavithrakb wrote: Dear Sir, Thanks so much.. now what's the solution? Should I increase the box size? Yes. If the protein protrudes "out" of the central image, then you will have an unstable system due to atomic overlap as well as violations of the minimum image convent

[gmx-users] Re: problem in g_membed

Dear Sir, Thanks so much.. now what's the solution? Should I increase the box size? Already I have centered the protein and fixed the POPE membrane size. Can you tell me how to increase the box size? or is there any other solution? -- View this message in context: http://gromacs.5086.x6.nabble

[gmx-users] Re: Re: unwrap trajectory file using -pbc nojump

gt; >> >> >> >> >> >> >> >> >> -- >> gmx-users mailing listgmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> * Please search the archive at >> http://www.gromacs.org/Support/Maili

Re: [gmx-users] Re: g_velacc

"g_integrate" should be "g_analyze" below. Sorry. On Fri, Jul 5, 2013 at 12:20 PM, Dr. Vitaly Chaban wrote: > Use this command line: > > -- g_velacc -nonormalize -acflen 2001 > -- g_integrate -f vac.xvg -integrate > -- Multiply the resulting value by 333.333, the result will be > self-diffusion

Re: [gmx-users] Re: g_velacc

Use this command line: -- g_velacc -nonormalize -acflen 2001 -- g_integrate -f vac.xvg -integrate -- Multiply the resulting value by 333.333, the result will be self-diffusion coefficient expressed as result * 10^(-9) m^2/s. The velocities should be written down at least every 10fs during MD. The

Re: [gmx-users] Re: g_velacc

On 2013-07-05 10:50, Ishwor wrote: I have taken the fit for 2ns in Einsteins curve to calculate the diffusion coefficient but when i take the values up to 100 ps for velocity auto correlation i get the matching result...Is it good to do such thing? i will be happy if you guide me. I have attached

[gmx-users] Re: g_velacc

I have taken the fit for 2ns in Einsteins curve to calculate the diffusion coefficient but when i take the values up to 100 ps for velocity auto correlation i get the matching result...Is it good to do such thing? i will be happy if you guide me. I have attached the graph of VAC herewith. Thanks

Re: [gmx-users] Re: Re: Lennard-Jones potential for protons

Yeah, ab initio MD sounds like the clearly best approach, and you will not do that with GROMACS. Mark On Thu, Jul 4, 2013 at 9:50 AM, Dr. Vitaly Chaban wrote: > why not to pick up a QM technique to study the "interaction"? > > Dr. Vitaly V. Chaban > > > On Thu, Jul 4, 2013 at 3:58 AM, Jong Wha L

Re: [gmx-users] Re: g_velacc

It would be nice to see plotted velocity autocorrelation function, VACF, which you integrate? The resulting diffusion constant looks crazy large, so there must be something rotten in the VACF. Dr. Vitaly V. Chaban On Thu, Jul 4, 2013 at 8:32 AM, Ishwor wrote: > I have really tried to calcul

Re: [gmx-users] Re: Re: Lennard-Jones potential for protons

why not to pick up a QM technique to study the "interaction"? Dr. Vitaly V. Chaban On Thu, Jul 4, 2013 at 3:58 AM, Jong Wha Lee wrote: > Thank you Mark and Vitaly. > > > > I understand that simulation of protons in the solution phase is > unphysical. > Though I haven't mentioned beforehand, I'm

Re: [gmx-users] Re: g_velacc

On 2013-07-04 08:32, Ishwor wrote: I have really tried to calculate diffusion coefficient using both commands but i cant find the comparable results. i have my *.mdp file as ;PREPROCESSING parameters tinit = 0 integrator = md dt =.002 nsteps =

[gmx-users] Re: g_velacc

I have really tried to calculate diffusion coefficient using both commands but i cant find the comparable results. i have my *.mdp file as ;PREPROCESSING parameters tinit = 0 integrator = md dt =.002 nsteps = 1 nstcomm = 1 ;O

[gmx-users] Re: Re: Lennard-Jones potential for protons

Thank you Mark and Vitaly. I understand that simulation of protons in the solution phase is unphysical. Though I haven't mentioned beforehand, I'm actually trying to simulate noncovalent interaction between a proton and a carbonyl oxygen in the gas phase. Could you give me any ideas how I may s

[gmx-users] Re: gmx-users problem in g_membed Digest, Vol 111, Issue 8

Dear Sir, thanks for the reply. what is the solution for this problem? can I just increase the box size? if so how? how to change the size without affecting the pope bilayer? regards, pavithra Message: 4 > Date: Tue, 2 Jul 2013 12:10:37 -0400 > From: Justin Lemkul > Subject: Re: [gmx-users] prob

[gmx-users] RE: Is non-linear data output/storage possible?

I see the same problem as Justin. The real problem lies here: mdrun -nt 4 -v -s 10step.tpr -c nonlinear.gro -e nonlinear.edr -x nonlinear.xtc -o nonlinear.trr -g nonlinear.log -cpi nonlinear.cpt -cpo nonlinear.cpt -rdd 2.5 Due to the '-cpi nonlinear.cpt' mdrun thinks the the time now the end

[gmx-users] RE: Is non-linear data output/storage possible?

So I would have to successively set tinit to the time of the last restart? Can I ask why that doesn't seem to be a problem when I am simply switching from saving every 10steps to every 100 steps? I am not at time zero then either, but at 2ps and grompp and mdrun did not complain then. Justin Lem

Re: [gmx-users] RE: Is non-linear data output/storage possible?

On Tue, Jul 2, 2013 at 1:23 PM, Neha wrote: > Hi, > > So the commands are: > > grompp -f 10step.mdp -p dppc_bilayer.top -o 10step.tpr -c dppc_bilayer.gro > > mdrun -nt 4 -s 10step.tpr -c nonlinear.gro -e nonlinear.edr -x > nonlinear.xtc > -o nonlinear.trr -g nonlinear.log -cpo nonlinear.cpt -rdd

[gmx-users] RE: Is non-linear data output/storage possible?

Hi, So the commands are: grompp -f 10step.mdp -p dppc_bilayer.top -o 10step.tpr -c dppc_bilayer.gro mdrun -nt 4 -s 10step.tpr -c nonlinear.gro -e nonlinear.edr -x nonlinear.xtc -o nonlinear.trr -g nonlinear.log -cpo nonlinear.cpt -rdd 2.5 grompp -f 100step.mdp -c 10step.tpr -p dppc_bilayer.top

Re: [gmx-users] RE: Is non-linear data output/storage possible?

On Tue, Jul 2, 2013 at 12:46 PM, Neha wrote: > So I tried doing this and ran into another problem. > > I made two mdp files, one that stored data every ten steps and one every > hundred steps > > I was thinking I would store data like this: > > 10 > 20 > 30 > . > . > . > 100 > 200 > . > . > . > 1

[gmx-users] RE: Is non-linear data output/storage possible?

So I tried doing this and ran into another problem. I made two mdp files, one that stored data every ten steps and one every hundred steps I was thinking I would store data like this: 10 20 30 . . . 100 200 . . . 1000 And then I would start another 'block' that would go 1010 1020 . . . 1100

[gmx-users] Re: Cite

Please keep all discussions on the mailing list. Others following the thread may be interested in it. The paper that came immediately to mind was dx.doi.org/10.1016/j.bpj.2010.04.062. -Justin On Tue, Jul 2, 2013 at 11:43 AM, wrote: > Hi, > > Sorry for use the email, I am new in the list and I

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