[gmx-users] Re: NPT and NVT simulations

Justin A. Lemkul jalemkul at vt.edu
Tue Jul 27 17:29:48 CEST 2010

Yes, if you define it in a [ constraints ] directive, and use "constraints = 
none" in your .mdp file, so that other bonds will not be converted to 
constraints, but the one you explicitly set in the topology will be used.


Nilesh Dhumal wrote:
> 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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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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