[gmx-users] Re: gmx-users Digest, Vol 98, Issue 42

Mark Abraham Mark.Abraham at anu.edu.au
Fri Jun 8 04:37:01 CEST 2012

On 7/06/2012 10:51 PM, PAVAN PAYGHAN wrote:
> Dear Mark,
> Thank you very much for the reply.
> To clarify , I have asked all the warning based questions to get 
> acknowledged with your expert opinion, apart from the manual based view.
> According to your suggestion  NPT with Position restraints is 
> messy,but still  I have seen lots of manual/tutorial (including Bevans 
> Lab ) suggesting the position restraining of protein during NVT as 
> well as NPT. That is the reason I have followed the same. Please 
> clarify your view on this matter.

It depends. If you need to fix your volume significantly, then trying to 
do so while using position restraints is somewhat asking for trouble and 
you should either give up position restraints or start again and get the 
volume closer to correct in the first place. (Those tutorials have 
likely managed this issue for you in the background.) Otherwise, use a 
different type of refcoord_scaling like the warning said. The existence 
of this mailing list is no substitute for doing basic background reading 
in (at least) the manual :-)


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