Hello
Can increase the emtol from 1000 to 10000 KJ mol - 1 nm-1?
subarna
________________________________
From: Mark Abraham <mark.abra...@anu.edu.au>
To: Discussion list for GROMACS users <gmx-users@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
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