[gmx-users] Why Position Restraint on Protein in NVT?

[Justin Lemkul]

On 10/18/12 12:06 PM, Arman M. Soufiani wrote:
> Dear all friends,
>
> I wonder why we should impose POSRES on the protein in the system while
> running NVT?! Shall we do so even for the system containing a short
> peptide?!

Velocity generation causes atoms to move randomly, which can impart nasty forces 
on your solute.  Restraining the solute helps preserve its structural integrity.

> What if I let the peptide, SOL+ions and my system's synthetic polymer apply
> T-coupling individually?
>

That depends on the size of each component.

http://www.gromacs.org/Documentation/Terminology/Thermostats

-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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