[gmx-users] NVT NPT restrains

[Justin Lemkul]

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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Justin A. Lemkul, Ph.D.
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Virginia Tech Department of Biochemistry

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