[gmx-users] Putting back the images of residues and atoms in the box

Hi there, I am trying to analyze a trajectory and some of the residues and atoms are seen as the image across the bound is there anyway to put them back in the centre box. Thanks Rohit -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Plea

Re: [gmx-users] Putting back the images of residues and atoms in the box

Rohit Farmer wrote: Hi there, I am trying to analyze a trajectory and some of the residues and atoms are seen as the image across the bound is there anyway to put them back in the centre box. http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions#Suggested_trjconv_

Re: [gmx-users] mdrun stuck with PME on BlueGene/P

On 5/12/2011 9:03 AM, Rongliang Wu wrote: Dear all, I have compiled the gromacs 4.5.5 version on BlueGene/P both on the front end and bgp using the following script : with the front end as an example --

[gmx-users] RMDS calculation

Dear all, I need to calculate the RMSD of a protein during time. So that I've calculated the trajectory; for the calculation which tool should I use? g_rms or g_rmsdist ? Which is the difference between these two tools? If I'm right the main difference is that with g_rms the structure at

Re: [gmx-users] RMDS calculation

Hi Valerio, Check the help for both tools. That explains it all. Oh, and you're not correct ;) Cheers, Tsjerk On Mon, Dec 5, 2011 at 4:42 PM, wrote: > Dear all, > > I need to calculate the RMSD of a protein during time. So that I've > calculated the trajectory; for the calculation which tool

[gmx-users] Re: MSD normalization

Hi, There is something interesting concerning these MSD calculations. If I treat Centre of Mass MSD if it'd be expressed not in nm^2/ps , but Angstroms^2/ps, I get ideally the same results as for mass-weighted ones. And it's true for all my three cases, in which I performed simulation of diffe

[gmx-users] setenv: Too many arguments

Dear All, I have installed gromacs 4.5.5 on ubuntu 11.04, however when I run command "source /usr/local/gromacs/bin/GMXRC" it gives the following message without doing anything. "setenv: Too many arguments" The logim shell is tcsh. Any help or suggestion would be much appreciated. Mehdi -- gm

[gmx-users] File input/output error pdb2gmx command

Hello. In GROMACS, within a terminal window on linux ubuntu, I am having trouble with a pdb2gmx command. The file I am trying to convert to a gmx file is called 1OTI.pdb. I type in pdb2gmx -f 1OTI.pdb -o 1OTI_processed.gro -water spce and hit enter. When it prompts me for a forcefield, I enter the

RE: [gmx-users] File input/output error pdb2gmx command

Though this looked familiar: http://lists.gromacs.org/pipermail/gmx-users/2011-November/066557.html What are the permissions for the file? Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville V

Re: [gmx-users] File input/output error pdb2gmx command

nbhut...@uci.edu wrote: Hello. In GROMACS, within a terminal window on linux ubuntu, I am having trouble with a pdb2gmx command. The file I am trying to convert to a gmx file is called 1OTI.pdb. I type in pdb2gmx -f 1OTI.pdb -o 1OTI_processed.gro -water spce and hit enter. When it prompts me f

Re: [gmx-users] Re: MSD normalization

On 6/12/2011 3:58 AM, Sławomir Stachura wrote: Hi, There is something interesting concerning these MSD calculations. If I treat Centre of Mass MSD if it'd be expressed not in nm^2/ps , but Angstroms^2/ps, I get ideally the same results as for mass-weighted ones. And it's true for all my thre

Re: [gmx-users] setenv: Too many arguments

On 6/12/2011 8:39 AM, Mehdi Talebzadeh Farooji wrote: Dear All, I have installed gromacs 4.5.5 on ubuntu 11.04, however when I run command "source /usr/local/gromacs/bin/GMXRC" it gives the following message without doing anything. "setenv: Too many arguments" The logim shell is tcsh. 4.5.

Re: [gmx-users] setenv: Too many arguments

I installed ARIA and CNS and it works; what do you mean from malformed csh? From: Mark Abraham To: Discussion list for GROMACS users Sent: Monday, December 5, 2011 7:53:17 PM Subject: Re: [gmx-users] setenv: Too many arguments On 6/12/2011 8:39 AM, Mehdi T

[gmx-users] Simulation in different PH

Dear all, How to run simulation in different PH? Kindly help to fix this problem. Thanks in advance... -- Regards, N. Sathishkumar, -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Sup

Re: [gmx-users] Simulation in different PH

Sathish wrote: Dear all, How to run simulation in different PH? Kindly help to fix this problem. Thanks in advance... The concept of "pH" is ill-defined for an MD system, the reasons for which have been discussed at length in recent days even (hint: please check the archive before posti

Re: [gmx-users] setenv: Too many arguments

On 6/12/2011 1:26 PM, Mehdi Talebzadeh Farooji wrote: I installed ARIA and CNS and it works; what do you mean from malformed csh? I think something is wrong with your environment and in the absence of further evidence the problem is likely nothing to do with GROMACS. In order to trouble-shoot