[gmx-users] Re: NPT and NVT simulations

[Nilesh Dhumal]

Can I put constraint on selected bond?
Nilesh

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
>> 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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