Tomy van Batis wrote:
On Tue, Dec 14, 2010 at 2:19 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@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
--
========================================
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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