[gmx-users] How to define Center of Mass velocity of a specific group
Tomy van Batis
tomyvanbatis at gmail.com
Wed Dec 15 16:25:50 CET 2010
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
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