subarna thakur wrote:
Hello
Can increase the emtol from 1000 to 10000 KJ mol ^- 1 nm^-1?
I wouldn't recommend it. That would be a really large maximum force, which
would probably cause your system to be very unstable. Look at your original
structure to see what might be wrong instead of just trying to find a way to
push forward.
-Justin
^
^subarna
------------------------------------------------------------------------
*From:* Mark Abraham <[email protected]>
*To:* Discussion list for GROMACS users <[email protected]>
*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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========================================
Justin A. Lemkul
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Virginia Tech
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