[gmx-users] An unexpected behavior of rdf calculated by the g_rdf command

Hello all gmx-users:    I have run a 100ns long MD simulation, the system is HAuCl4 acid solution, which contains one [AuCl4]- cluster and 503 water moleculars, and calculated the rdf by using the g_rdf command as follow: g_rdf -f yqqmd.trr -s yqqmd.tpr -n yqq.ndx -o rdf.xvg -cn cn.xvg -rdf a

Re: [gmx-users] (no subject)

On 27/11/09 3:15 AM, pawan raghav wrote: I have used GROMACS 4.0.5 on windows can anyone tell me about how to get em.mdp, and pr.mdp file for my protein. -- Pawan Hi, A good place to start and learn about mdp files is http://www.gromacs.org/Documentation/Tutorials. You can find lot of tuto

Re: [gmx-users] domain decomposition errors

Thanks david: the chrash error is : Making 2D domain decomposition 4 x 2 x 1 starting mdrun 'PLASMEPSIN 2 in water' 3000 steps, 6.0 ps. Step 33, time 0.066 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 1.084460, max 31.492893 (between atoms 3168 and 3169) bonds that r

Re: [gmx-users] domain decomposition errors

pedro alberto valiente flores wrote: Hi gromacs users: I' am trying to run a MD simulation of PlmII+Inhibitor system in cubic box (59002 atoms) with gromacs 4.0.5 on 8 processors, but my simulation crashes. In attach are files.tgz which contains the log (PlmII+PepstatinA_free.log) and error file

[gmx-users] domain decomposition errors

Hi gromacs users: I' am trying to run a MD simulation of PlmII+Inhibitor system in cubic box (59002 atoms) with gromacs 4.0.5 on 8 processors, but my simulation crashes. In attach are files.tgz which contains the log (PlmII+PepstatinA_free.log) and error files (BSA.err.%j). However, I can run the

[gmx-users] Unexpected behavior of g_msd

Hi Berk, I am thinking that you mean that MSD is a function of the time differences and the number of time differences. In other words, if the simulation is too short, then GROMACS would not have enough time differences to accurately calculate a diffusion constant since the slope of the msd versus

Re: [gmx-users] Simulation at unrealistic temperatures

Possibly your water is boiling? YOu could try with NVT. Neha Bharat Gajaria wrote: Dear List, I m trying to run an NPT simulation at 600K which looks unrealistic. I m running minimization followed by anealing and then NPT simulation (mdp files are attached). The job keeps running but after

Re: [gmx-users] water molecule not settled.........

YOu have atomic overlaps or not energy minimized your starting structure. Best, Jochen pavan payghan wrote: hi ... while running mdrun im getting an error water molecule is not settled there is only single such water molecule what should be possible way

[gmx-users] (no subject)

I have used GROMACS 4.0.5 on windows can anyone tell me about how to get em.mdp, and pr.mdp file for my protein. -- Pawan -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posti

[gmx-users] What is the current wisdom on energy leak?

Dear Gromacs users, I am a little new fellow in this community, and many things still I don't know. I am trying to parametrize a coarse-grained FF for polymer simulations, without solvent. A collegue of mine advised me, just to be sure, to check for possible energy leak artefacts. To do that he t

Re: [gmx-users] Simulation at unrealistic temperatures

Maybe the system is exploding? Have you looked at the movie? And I agree with you that it might be unrealistic to do simulation at 600K using a force-field which was parametrized at 300K. Omer. On Thu, Nov 26, 2009 at 05:56, Neha Bharat Gajaria wrote: > > Dear List, > > I m trying to run an NPT s

RE: [gmx-users] Unexpected behavior of g_msd

NO! The MSD is NOT a function of the trajectory time! The MSD is a function of time differences. For example: if trestart=10 and -b=60 then MSD(4) in the output is the average of the the MSD between 64 and 68, 74 and 78, 84 and 88, etc. Berk > Date: Thu, 26 Nov 2009 01:52:17 -0800 > From: darre.

[gmx-users] Unexpected behavior of g_msd

Hi Berk, Yes, I am aware of the -b and -e options in g_msd but was wondering why the output said "Fitting from 4 to 35.9 ps" when I selected the time period from 60 to 100 ps. It appears that the output comment actually meant that it was fitting from 60+4 to 60+35.9 ps, but this is not clear to

[gmx-users] water molecule not settled.........

hi ... while running mdrun im getting an error water molecule is not settled there is only single such water molecule what should be possible way out...? the same system when i run in previous version of gromacs it showed wrote pdb files with previous & current

RE: [gmx-users] Unexpected behavior of g_msd

Hi, You don't need trjconv, g_msd has options -b and -e. But the regression is obviously done on the time differences and not on the frame times. MSD is a function of a time difference, not of simulation time. Berk > Date: Thu, 26 Nov 2009 13:24:12 +1100 > From: dallas.war...@pharm.monash.edu.

[gmx-users] Buffer Overflow Problem on Ubuntu Linux

Hi, I installed gromacs 3.3.3 on Ubuntu Linux 9.10 running on a Intel(R) Core(TM)2 Quad CPU @ 2.40GHz w/ 4 GB RAM. I am getting the following errors for any of the gromacs commands, even when I am using the -h option to list the options available for that command. I removed the installation and