Hi Justin
I see the point of restraining heavy atoms in NPT.The problem is that; no posre
are included in the top file generated by Acpype, any suggestion to overcome
that? Kind Regards,Ahmed
From: Justin Lemkul <jalem...@vt.edu>
To: gmx-us...@gromacs.org
Sent: Tuesday, February 20, 2018 7:55 PM
Subject: Re: [gmx-users] NVT NPT restrains
On 2/20/18 1:47 PM, Ahmed Mashaly wrote:
> Hi
>
> About the restrains, I see that it is necessary for NVT and NPT.
> For the .top and .gro produced by Acpype,
> https://drive.google.com/open?id=1K5IqAWb1_jXUfUPDjDtkOX2l8GuzbprM
>
> I don't have porse.itp nor anything related to restrain in the .top file,
> only for water
>
> #ifdef FLEXIBLE
> [ bonds ]
> ; i j funct length force.c.
> 1 2 1 0.09572 462750.4 0.09572 462750.4
> 1 3 1 0.09572 462750.4 0.09572 462750.4
>
>
> So what shall I do in this case? and what is the ideal time for NVT and NPT
Restraints are typically applied to solute heavy atoms to prevent
distortion from initial, artificial configurations. It is very rare to
need to restrain water, as that defeats the purpose of equilibration,
which is primarily to allow the solvent to relax and achieve the desired
state.
-Justin
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Virginia Tech Department of Biochemistry
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