[gmx-users] energy minimization

[subarna thakur]

Hello
Can increase the emtol from 1000 to 10000 KJ mol - 1 nm-1?
 
subarna



________________________________
From: Mark Abraham <Mark.Abraham at anu.edu.au>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Thu, 10 December, 2009 2:33:23 PM
Subject: Re: [gmx-users] energy minimization

subarna thakur wrote:
> I am doing the energy minimization of a protein using the following keywords in em.mdp file-
> cpp                =  /usr/bin/cpp
> define              =  -DFLEX_SPC
> constraints        =  none
> integrator          =  steep
> nsteps              =  3000
> ;
> ;    Energy minimizing stuff
> ;
> emtol              =  1000
> emstep              =  0.01
> 
> nstcomm            =  1
> ns_type            =  grid
> rlist              =  1
> coulombtype        =  PME
> rcoulomb            =  1.0
> rvdw                =  1.0
> Tcoupl              =  no
> Pcoupl              =  no
> gen_vel            =  no
> 
> -----------------------------------------------------------------
> I am getting the ouput as following---------
> Steepest Descents converged to machine precision in 67 steps,
> but did not reach the requested Fmax < 1000.
> Potential Energy  = -4.0967048e+06
> Maximum force    =  3.7720719e+04 on atom 5530
> Norm of force    =  1.7014005e+02
> -----------------------------
> Can anybody suggest what changes I can make

Well you can play with the EM step size, or see if atom 5530 looks unhappy, or you can move on to your equilibration and hope nothing's seriously wrong.

Mark
-- gmx-users mailing list    gmx-users at gromacs.org
http://lists.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



      The INTERNET now has a personality. YOURS! See your Yahoo! Homepage. http://in.yahoo.com/
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20091210/9c3f51af/attachment.html>