[gmx-users] Re: NPT and NVT simulations

Vitaly Chaban vvchaban at gmail.com
Mon Jul 26 05:33:53 CEST 2010

1. Using freezegrps is not generally a good idea to fix a bond length.
Look at the constraints mechenism better. Or just try a bigger force
constant in topology.

2. NPT and freezegrps do not interact correctly, since freezegrps just
freezes any changes of atom positions, so they are not rescaled even
if the box size is changed in NPT.

3. Anyway, I think you have defined incorrect groups if your atoms of
interest are still movable. Check a diffusion constant of your bonded
atoms, it should be zero in the case of freezegrps.

Dr. Vitaly Chaban

> I am trying to freeze a bond (3.5 A) in my system.  I used the index file
> to define group and I added this two lines in my .mdp file.
> freezegrps         = PA NE
> freezedim   = Y Y Y Y Y Y
> I used g_dist to verify the distance between the freezing atoms. During
> the NVT simulation the distace is around 3.449 A and its constant though
> out the simulation. For NPT simulation the distance varies from 3.449 to
> 3.1.
> Can you tell why distance changes in NPT not in NVT.
> How can I freeze a bond om NPT simulation?

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