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

[Tomy van Batis]

On Tue, Dec 14, 2010 at 2:19 PM, Justin A. Lemkul <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?

Many thanks

Chrysostomos
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20101215/ea116492/attachment.html>