On Tue, Dec 14, 2010 at 2:19 PM, Justin A. Lemkul <[email protected]> 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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