[gmx-users] unstable system
shima_arasteh2001 at yahoo.com
Fri Apr 19 20:49:53 CEST 2013
The energy minimization has been done and the result is as follow:
Steepest Descents converged to Fmax < 100 in 8971 steps
Potential Energy = -1.5253394e+06
Maximum force = 9.2729095e+01 on atom 4719
Norm of force = 3.5977371e+00
But by running mdrun, I get this fatal error:
1 particles communicated to PME node 4 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x.
So needs more npt?
Thanks for your suggestions in advance.
----- Original Message -----
From: Justin Lemkul <jalemkul at vt.edu>
To: Shima Arasteh <shima_arasteh2001 at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Friday, April 19, 2013 10:02 PM
Subject: Re: [gmx-users] unstable system
On 4/19/13 1:18 PM, Shima Arasteh wrote:
> Lets check the minim.mdp settings:
> ( ff applied is charmm36)
> define = -DPOSRES
> integrator = steep
> emtol = 100.0
> emstep = 0.01
> nsteps = 50000
> nstlist = 1
> ns_type = grid
> rlist = 1.2
> rlistlong = 1.4
> coulombtype = PME
> rcoulomb = 1.2
> rvdw = 1.2
> vdwtype = switch
> rvdw_switch = 1.0
> pbc = xyz
> I would be grateful for your suggestions.
I see no reason to use restraints (doing so defeats the purpose of EM), but
otherwise the settings are fine.
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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