[gmx-users] unstable system

[Shima Arasteh]

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


 
Sincerely,
Shima


----- Original Message -----
From: Justin Lemkul <jalemkul at vt.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Cc: 
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

-- 
========================================

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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