[gmx-users] Need protein-ligand free energy calculation tutorial

Dear Gromacs users -- Iam trying to perform free energy calculation for protein-ligand complex. --Can any one plz suggess an appropriate tutorial to be follow to perform this analysis -- Thanks Regards N.NagaSundaram -- gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] Stopping protein jumping inside box

Hi Plz try -pbc nojump option...It may work On Wed, Feb 13, 2013 at 5:29 AM, 라지브간디 ra...@kaist.ac.kr wrote: Dear gmx users, I need to stop my protein jumping inside box. I have used -pbc mol -ur compact -center command too but still the protein gets moving from one place to other.

[gmx-users] How to analysis 10 ns from 20 ns simulation

Dear users I performed 20 ns simulation for protein complex. After 10 ns only my system obtained equilibration state . I would like to analyze last 10 ns from the trajectory file.I got problem to generate last 10 ns xtc file from the 20 ns trr file.

[gmx-users] Regarding append the run

Dear friends Unfortunately my MD run got stopped. While i tried to append the run with command line mdrun -s fws_md.tpr -cp state.cpt -append, its not get appending, its again get restart. What should be the problem.I need to append my run. --

Re: [gmx-users] Regarding append the run

Thanks justin got it... On Wed, Oct 3, 2012 at 4:10 AM, Justin Lemkul jalem...@vt.edu wrote: On 10/3/12 6:10 AM, naga sundar wrote: Dear friends Unfortunately my MD run got stopped. While i tried to append the run with command line mdrun -s fws_md.tpr -cp

Re: [gmx-users] xmgrace graphs

Dear Pramod use the command xmgrace -nxy file1.xvg file2.xvg Instead of file1 and file2 use ur file name. On Tue, Oct 2, 2012 at 8:49 PM, ram bio rmbio...@gmail.com wrote: Dear Gromacs users, I am trying to find inter atomic distances

Re: [gmx-users] Regarding RMSD analysis result

-Nachricht Datum: Mon, 24 Sep 2012 04:32:33 -0700 Von: naga sundar naga25sun...@gmail.com An: Discussion list for GROMACS users gmx-users@gromacs.org Betreff: Re: [gmx-users] Regarding RMSD analysis result Dear justin Thanks for ur suggestions

Re: [gmx-users] Regarding RMSD analysis result

by subtracting half the x/y dimension of the box from its coordinates and re-calculate the rmsd , but I think trjconv would do it as well. Felipe On 09/25/2012 09:22 AM, naga sundar wrote: Dear justin http://rmsdnagasundaram.**blogspot.in/http://rmsdnagasundaram.blogspot.in

[gmx-users] Regarding RMSD analysis result

Dear gromacs users We performed MD simulation analysis for native and mutant models of protein-protein complexes. From 20 ns simulation trajectory, we generated RMSD graph for one native and three mutant complexes. For native complex in the entire simulation period, we observed a

Re: [gmx-users] Regarding RMSD analysis result

/S0006291X08020792. Overall, all the factors are supporting our results. So shall we take this RMSD analysis as good result . Even after repeating the 20 ns MD simulation two times i got the same results. On Mon, Sep 24, 2012 at 3:41 AM, Justin Lemkul jalem...@vt.edu wrote: On 9/24/12 6:24 AM, naga

Re: [gmx-users] Residue 'UNK' not found in residue topology database

Dear simone I think so u r using the same pr.mdp and md.mdp files what u created initially. So open both the mdp files replace DRG with UNK and the try sure it will work out. On Tue, Sep 18, 2012 at 9:44 AM, Justin Lemkul jalem...@vt.edu wrote: On 9/18/12 12:42 PM, SIMONE

[gmx-users] Regarding RMSD graph nalysis

Dear gromacs users I run 20 ns MD simulation for protein mutant complexes. In RMSD analysis at ~9 ns sudden increase in the deviation was observed from 0.2 nm to 1.7 nm and immediate fall was observed. I rerun the 20 ns simulation for the same molecule with same procedure. While analyzing the