[gmx-users] parameter on Energy Minimization

Liu Shiyong liushiyong at gmail.com
Wed Mar 12 00:23:15 CET 2008

Thanks Mark and  Justin.

 I did experiment with the  following  editconf.    It works.  Thanks.

  editconf -f ${file}.gro -o ${file}_box.gro -d 0.75 -bt cubic

    By the way,  how to select box size automatically ?  I just gave an
arbitrary number: 0.75

   Another question is how to get the structure with lowest energy  from
*.trr ?

  When I used the following command:
   trjconv  -f ${file}.minim_traj.trr -s ${file}.input.tpr -o

  It outputs 15 MODELS with   t= 125.00000 t= 252.00000, t= 379.00000 ,
...t= 2001.00000

 I guess  t= 2001.00000 has the lowest energy.


On Tue, Mar 11, 2008 at 5:58 PM, Mark Abraham <mark.abraham at anu.edu.au>

> > Hi,
> >
> > I used a script given below for energy minimization of  a native
> > protein-protein complex 1akj.
> >
> > I removed HETATMs and water molecules from the structure, and the
> > minimized
> > structure  (1akj_oplsaa.minim_traj.pdb) with epsilon_r=80.
> > Then I used rasmol to check the result.  The ligand is ran away from
> > receptor.
> >  rasmol 1akj_oplsaa.minim_traj.pdb
> As Justin said, you might well be observing a PBC artefact. Having not
> turned off PBC in your .mdp file, or used editconf to change the size of
> the box that pdb2gmx chooses, then your EM is probably using defaults that
> you'd rather not use.
> > Then I tried the larger epsilon_r           =  800000.0, and got very
> > similar result. I mean that for two substantially different values of
> the
> > epsilon_r minimization gives absolutely the same final positions of the
> > ligand.
> Being good scientists, we deduce that the approximate location of the
> local energy minimum from this starting point is not dependent on the
> dielectic of the medium. :-)
> > I also tried difference forcefield encads, encadv, G43a1, G43a2, G43b1,
> > G45a3, G53a5, G53a6,  gmx, oplsaa.
> > I also got similar result.
> Likewise.
> Mark
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Shiyong Liu
Research Assistant
center for bioinformatics in the university of kansas
Lab: (785)864-1962
Email: syliu at ku.edu (shiyongliu at ku.edu or liushiyong at ku.edu)
Homepage: http://www.people.ku.edu/~syliu
Lab: http://vakser.bioinformatics.ku.edu/people
Phone: (785) 864-1962
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20080311/d6349f70/attachment.html>

More information about the gromacs.org_gmx-users mailing list