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

[Justin A. Lemkul]

Tomy van Batis wrote:
> 
> 
> On Tue, Dec 14, 2010 at 2:19 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     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 <http://www.gromacs.org/Support/Mailing_Lists>
> 
> 
> Dear Justin
> 
> I found how to freeze the group that I want, but what I can't find is 
> how to use the position restrains.
> 
> I created just 1 chain. As I can see in my* topol.top* file it's 
> automatically included the *posre.itp* file. I inserted in my *.mdp* 
> file the following line:
>  define = -DPOSRE
> 
> but after running NVT for few steps I see that the chain is still moving 
> a lot.
> 
> I can't find any example in the manual or in the internet. Can you 
> please tell me what to do?
> 

If the topology was written by pdb2gmx, the #define statement should be "#define 
POSRES," not "#define POSRE," so your define statement in the .mdp file is 
incorrect.

-Justin

> Many thanks
> 
> 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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