[gmx-users] grommp warning

[Shima Arasteh]

OK, thanks.
But please let me know something:
Is the "pressure coupling with absolute position restraints" is an option to fix a volume significantly? If yes, then It's me to think about  keeping fix the volume of my system or not.
Thanks, believe me I got this point through the mailing list :-) 


Sincerely,
Shima


________________________________
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: Tuesday, August 14, 2012 12:08 AM
Subject: Re: [gmx-users] grommp warning



On 8/13/12 12:36 PM, Shima Arasteh wrote:
> Dear gmx users,
>
> I'm simulating a system of protein and water. In NPT equilibration step, I get the error of too many warnings.
> Anybody knows about this warning?
>

Yes, and there are several posts in the list archive explaining its origin, 
interpretation, and solution.

> The warning is :
>
> WARNING 1 [file NPT.mdp]:
>    You are using pressure coupling with absolute position restraints, this
>    will give artifacts. Use the refcoord_scaling option.
>

You need to set a sensible value for the quoted option.  Consult the manual and 
list archive.

-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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