[gmx-users] unstable system

[Shima Arasteh]

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.

 
Sincerely,
Shima


----- 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>
Cc: 
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

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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