[gmx-users] unstable system

Shima Arasteh shima_arasteh2001 at yahoo.com
Fri Apr 19 20:57:46 CEST 2013

Thanks so much for your replies. I appreciate you.
Do you think that more NPT equilibration might solve the problem? or wont work?


----- Original Message -----
From: Justin Lemkul <jalemkul at vt.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Friday, April 19, 2013 11:23 PM
Subject: Re: [gmx-users] unstable system

On 4/19/13 2:49 PM, Shima Arasteh wrote:
> 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?

I have no idea what this means.  The minimization looks perfect.  Continue with 
whatever equilibration scheme you think is appropriate.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080

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