[gmx-users] Re: NPT and NVT simulations
ndhumal at andrew.cmu.edu
Tue Jul 27 17:27:28 CEST 2010
Can I put constraint on selected bond?
On Sun, July 25, 2010 11:33 pm, Vitaly Chaban wrote:
> 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
>> Can you tell why distance changes in NPT not in NVT.
>> How can I freeze a bond om NPT simulation?
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