RE: [gmx-users] help: z-direction component of box vector becomes 0.00000 when using pdc = xy after

Hi, I tried to reproduce this, but I did not succeed. mdrun always seems to write the correct z size in all output files. Are you sure mdrun outputs a file (and which file, if so), or is it another Gromacs program that produced the file with 0 z size? You can simply manually correct the size in

[gmx-users] extending simulations

Dear all, I'd need to have a clarification about how to extend a simulation made using GROMACS 4 that has been interrupted on a system due to walltime expiration. On the Wiki section I see: "A simulation that has completed is extended using tpbconv, mdrun and checkpoint files (.cpt). A simulation

Re:[gmx-users] extending simulations

You can use the mdrun command: How to restart a crashed run. The mdrun program now uses a very handy checkpointing feature. Restarting crashed runs is easy with mdrun. mdrun -s prev.tpr -f prev.trr -e prev.edr -o prev.trr –g prev.log –cpi -append 在2009-05-06，"Anna Marabotti" 写道： >Dear al

Re: [gmx-users] extending simulations

Anna Marabotti wrote: Dear all, I'd need to have a clarification about how to extend a simulation made using GROMACS 4 that has been interrupted on a system due to walltime expiration. On the Wiki section I see: "A simulation that has completed is extended using tpbconv, mdrun and checkpoint

Re: [gmx-users] g_angle - Order of Legendre polynomial for ACF - BUG ?

Dear Dennis, I believe your problem is due to the fact that when the autocorrelation is done on a dihedral angle a cos function is used instead of the angle itself. This is good to account for periodicity. This function is not implemented in the -P 1 2 3 ... if I recall correctly. I thin

[gmx-users] Can we abstract any frame from the trajectory file(trr) and save it as a gro file?

Dear gmx users, I have performed NPT MD simulations and achieved a trr file. Now I want to start another NVT MD simulations using some frame as the initial configuration. But I was puzzled by how to abstract any frame from the trajectory file and to save it as a gro file. Please give me some

Re: [gmx-users] g_angle - Order of Legendre polynomial for ACF - BUG ?

Dennis Glass wrote: Hello, I am facing a problem with g_angle. I want to analyse some dihedrals. When calculating the autocorrelation function, g_angle crashes if I want to use a Legendre polynomial for the ACF. Can I somehow handle this problem? The legendre polynomial only applies to ve

Re: [gmx-users] Can we abstract any frame from the trajectory file(trr) and save it as a gro file?

wuxiao wrote: > Dear gmx users, > I have performed NPT MD simulations and achieved a trr file. Now I > want to start another NVT MD simulations using some frame as the initial > configuration. But I was puzzled by how to abstract any frame from the > trajectory file and to save it as a gro f

[gmx-users] problem with mpi

Hi,I am trying to use parallel gromacs3.3.3  mdrun programme  .I have installed mpich2 in our quadcore machine. But I am having 3 problems:   1. The scaling is very poor among 4 cores: varies between 30-70 %.    2. If I run the mdrun_mpi in background, the output log file cites following error: 

[gmx-users] Questions to pullx.xvg

Hi all, what are the meanings of the columns X and dX? From the manual i think the first column X should be the position of the pull-group. But in my case it is the position of the reference group, so i'm a little bit troubled. And what is dX? For me it looks that this is the vector from the refere

RE: [gmx-users] Questions to pullx.xvg

Hi, You are completely right. This should have been documented somewhere. But I changed this after the 4.0 release in on of the minor releases, therefore this could not be documented. In pullx.xvg X 0 means the coordinate(s) of group 0 and dX 1 the vector from group 0 to group 1. Berk > Date: W

[gmx-users] mpi problem

Hi,I am trying to use parallel gromacs3.3.3  mdrun programme  .I have installed mpich2 in our quadcore machine. But I am having 3 problems:   1. The scaling is very poor among 4 cores: varies between 30-70 %.    2. If I run the mdrun_mpi in background, the output log file cites following error: 

Re: [gmx-users] g_angle - Order of Legendre polynomial for ACF - BUG ?

Dennis Glass wrote: Hello, I am facing a problem with g_angle. I want to analyse some dihedrals. When calculating the autocorrelation function, g_angle crashes if I want to use a Legendre polynomial for the ACF. Can I somehow handle this problem? The legendre polynomial only applies to vec

[gmx-users] How to concatenate several input trajector y files in sorted order in GMX4.01

Dear all: I extended a mdrun in GMX4.01,and the two trajectory files can not been concatenated,i.e.the "trjcat"command is invalid in GMX4.01. How to solve this question? Thank you very much! Sincerely Zhang,Rui ShanDong university___ gmx-users maili

Re: [gmx-users] How to concatenate severa l input trajectory files in sorted order in GM X4.01

zhang wrote: Dear all: I extended a mdrun in GMX4.01,and the two trajectory files can not been concatenated,i.e.the "trjcat"command is invalid in GMX4.01. How to solve this question? Do not use 4.0.1; it was inadvertently crippled during development. Upgrade to 4.0.4 and start over. -Ju

RE: [gmx-users] Questions to pullx.xvg

Hi, thanks for the clarification. Thomas > > > Hi, > > You are completely right. > This should have been documented somewhere. > But I changed this after the 4.0 release in on of the minor releases, > therefore this could not be documented. > In pullx.xvg X 0 means the coordinate(s) of group 0

RE: [gmx-users] extending simulations

If you want to extend your simulation, simply use the 'append' command. : mdrun -append yes -cpi state.cpt Extending a simulation is quite simple. However, if your trajectory file is larger than 2GB, you are going to have a problem. I tested it a few weeks ago and found out that the 'append' opti

RE: [gmx-users] extending simulations

dear sir/Madam   i want to work in mopac/gromacs interface for that i have downloaded mopac 7-1.10 tar.gz when run ./configure in the TAR file in command  prompt of redhat linux EL5 to install mopac  i got the the following error in command prompt bash: ./configure: /bin/sh^M: bad interpreter:

Re: [gmx-users] extending simulations

Please start a new thread if you are asking a new question; it will help get the attention of someone who may be interested in helping you, but who may not have any comments on the "extending simulations" thread. vidhya sankar wrote: dear sir/Madam i want to work in mopac/gromacs interface

[gmx-users] problem with particle decomposition in gromacs 4.0.4

Hi, I am trying particle decomposition with gromacs 4.0.4 for a small polymer (20 atoms) in SPC/E water. Unfortunately every run crashes at the very beginning without any useful error message, when I use version 4.0.4 with option -pd. Whereas everything remaining same it's still running fine in ve

RE: [gmx-users] problem with particle decomposition in gromacs 4.0.4

Hi, Are the crashes with plain 4.0.4, or 4.0.4 with PLUMED? I have not heard of crashes in 4.0.4 with particle decomposition, so it might have to do with the link with PLUMED. Have you tried running 4.0.4 in single processor? If plain Gromacs 4.0.4 crahes on your system with PD, please file a r

[gmx-users] Martini+elastic network

Dear all, I am trying to run an energy minimization of a protein using Martini model + Elastic Network. I created correctly the itp file adding the constrain for the elastic network. when I try to submit the job on 32 processors I get the following: __

Re: [gmx-users] Martini+elastic network

Enrico Spiga wrote: Dear all, I am trying to run an energy minimization of a protein using Martini model + Elastic Network. I created correctly the itp file adding the constrain for the elastic network. when I try to submit the job on 32 processors I get the following: the given box and

RE: [gmx-users] problem with particle decomposition in gromacs 4.0.4

Yes, I have encountered this crash with plain Gromacs 4.0.4 as well. I have not tried single processor, but with domain decomposition it runs fine. I am not sure whether it has got to do anything with our parallel architecture though. In any case, I shall file a report after I reproduce this f

[gmx-users] P-coupling in vacuum, inflexibility

Dear colleagues, I want to put in my cell a lot of molecules (f.e., 32 lipids), and I make for it a very big box, put my molecules into this box (without water) and then do simulations with pressure coupling to make my box smaller. So, how can I make my molecules inflexible? if I set links or s

Re: [gmx-users] P-coupling in vacuum, inflexibility

Hi Pavel, It seems that your molecules are broken over the periodic boundaries. Make sure that you set up your coordinates and topology file correctly. Cheers, Tsjerk 2009/5/6 Pavel Semenyuk : > Dear colleagues, > > I want to put in my cell a lot of molecules (f.e., 32 lipids), and I make for

[gmx-users] Energy minimization error by GMX 4.0.4

Dear All: I just installed the gmx_4.0.4 double precision. When I do EM, the grompp_d command has no problem. However after I submit the job, it gives me the following error. Anyone can tell me what is the problem which may cause that? By the way, in 4.0.4, it can only use 4 CPU, right? Can we s

[gmx-users] Re: Energy minimization error by GMX 4.0.4

Also I have checked that it works well in gmx_3.3.3. Anyone can tell me what is the problem ? Thanks! On Wed, May 6, 2009 at 1:47 PM, Yanmei Song wrote: > Dear All: > > I just installed the gmx_4.0.4 double precision. > > When I do EM, the grompp_d command has no problem. However after I submit

Re: [gmx-users] Energy minimization error by GMX 4.0.4

Yanmei Song wrote: Dear All: I just installed the gmx_4.0.4 double precision. When I do EM, the grompp_d command has no problem. However after I submit the job, it gives me the following error. Anyone can tell me what is the problem which may cause that? By the way, in 4.0.4, it can only

Re: [gmx-users] Energy minimization error by GMX 4.0.4

Justin A. Lemkul wrote: Yanmei Song wrote: Dear All: I just installed the gmx_4.0.4 double precision. When I do EM, the grompp_d command has no problem. However after I submit the job, it gives me the following error. Anyone can tell me what is the problem which may cause that? By the

Re: [gmx-users] Energy minimization error by GMX 4.0.4

Yanmei Song wrote: Dear All: I just installed the gmx_4.0.4 double precision. When I do EM, the grompp_d command has no problem. However after I submit the job, it gives me the following error. Anyone can tell me what is the problem which may cause that? You're using a new .tpr with an o

Re: [gmx-users] problem with mpi

jagannath mondal wrote: Hi, I am trying to use parallel gromacs3.3.3 mdrun programme .I have installed mpich2 in our quadcore machine. But I am having 3 problems: 1. The scaling is very poor among 4 cores: varies between 30-70 %. 2. If I run the mdrun_mpi in background, the output log

Re: [gmx-users] Energy minimization error by GMX 4.0.4

Thank you so much for all the helpful response. On Wed, May 6, 2009 at 4:59 PM, Mark Abraham wrote: > Yanmei Song wrote: > >> Dear All: >> >> I just installed the gmx_4.0.4 double precision. >> >> When I do EM, the grompp_d command has no problem. However after I submit >> the job, it gives me t

[gmx-users] modify lennard jones parameters to time-dependent

Dear all, Is there any way to modify the LJ potential as a time dependent value, e.g. V(r)=4*e(t)*((sigma/r)^12-(sigma/r)^6), here e(t) is time-dependent, for instance, e(t)=e0*cos(w*t)? If the code needs to be modified, which C file should I find? Xinghua

Re: [gmx-users] modify lennard jones parameters to time-dependent

Xinghua Shi wrote: Dear all, Is there any way to modify the LJ potential as a time dependent value, e.g. V(r)=4*e(t)*((sigma/r)^12-(sigma/r)^6), here e(t) is time-dependent, for instance, e(t)=e0*cos(w*t)? If the code needs to be modified, which C file should I find? Simplest would be to gener

[gmx-users] itp and gro files

I was wondering if the order of sites in .gro file should be the same as in .itp file. Payman ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.

Re: [gmx-users] itp and gro files

Payman Pirzadeh wrote: I was wondering if the order of sites in .gro file should be the same as in .itp file. Yes, otherwise, you will see grompp warnings indicating that atom names in the .top and .gro do not match. -Justin Payman --

RE: [gmx-users] itp and gro files

Thank you very much. Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: May 6, 2009 8:25 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] itp and gro files Payman Pirzadeh wrote: > I

RE: [gmx-users] Can we abstract any frame from the trajectory file(trr) and save it as a gro file?

You can use trjconv to extract a frame from the trajectory, e.g. trjconv �Cf xxx.trr �Co xxx.gro �Cb ttt �Ce ttt From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of wuxiao Sent: Wednesday, May 06, 2009 8:42 AM To: gmx-users

Re: [gmx-users] modify lennard jones parameters to time-dependent

Mark Abraham wrote: Xinghua Shi wrote: Dear all, Is there any way to modify the LJ potential as a time dependent value, e.g. V(r)=4*e(t)*((sigma/r)^12-(sigma/r)^6), here e(t) is time-dependent, for instance, e(t)=e0*cos(w*t)? If the code needs to be modified, which C file should I find? In yo