[gmx-users] How to define Center of Mass velocity of a specific group

[Justin A. Lemkul]

Tomy van Batis wrote:
> Dear all
> 
> I have a system consisting of 2 substrates (20 nm distance between them) 
> and inside them there are polymer chains. I would like during my NVT 
> simulations the substrates NOT to move (I suppose I have to put  the 
> velocity of the COM of it's substrate to be zero).
> 
> Does anyone know how to do that? 
> 

The simplest way is to just use position restraints.  The positions may change 
very slightly, but not a noticeable amount.

If you absolutely require no movement at all, use freezegrps in the .mdp file.

-Justin

> Thanks in advance
> Chrysostomos
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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