[gmx-users] position restraint dynamics

[Justin A. Lemkul]

bhargavi ch wrote:
>  
> Hi..dear gromacs users...How do we decide the ideal time to run PR??we 
> are simulating a protein of 260 amino acids  which is a tirmer...we have 
> done the PR for 10 ps first time and 100ps for the second ...i had 
> observed a stable graph in the latter compared with the other...and on 
> what factors does do we decide the time interval in PR
>  

It depends on your ensemble.  If you're using NVT, run PR long enough to see the 
temperature stabilize.  If you're running NPT, run PR until both pressure and 
temperature stabilize.

-Justin

> lucky.
> 
> 
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-- 
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Justin A. Lemkul
Graduate Research Assistant
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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