[gmx-users] Re: gmx-users Digest, Vol 84, Issue 62

Vitaly Chaban vvchaban at gmail.com
Thu Apr 7 21:40:34 CEST 2011

> Hello,
> I think it would be very good to have this feature in gromacs. In fact I've
> recently had some problems with constraining some species in my simulations.
> Finally I've sorted out with shake but your solution seems to me less
> problematic.
> Thanks in advance.
> Best,
> Gyorgy
> Quoting ms <devicerandom at gmail.com>:
>> On 27/03/11 23:02, Adam Herbst wrote:
>>> Hi all,
>>> I have seen a few posts on gmx-users indicating a desire to treat
>>> certain atom groups as rigid bodies in MD simulations.  I just started
>>> implementing this, and so far I have it working for translational forces
>>> (not rotation, though this should be simple to add), even when the group
>>> is split over multiple processors.  At the moment I have the rigid body
>>> groups specified as freeze groups in the mdp file, but there could be a
>>> separate option.  Would anyone else find this useful?  The problem is
>>> that: (a) I am modifying GROMACS 4.5.1, so I am some months out of date,
>>> and (b) my code is probably not to spec.  If it is worthwhile, I can
>>> restart from 4.5.4 (the code modifications are quite small) and make an
>>> effort to conform to coding standard.  Best,
>>> Adam Herbst
>> I would love that!!
>> --Massimo Sandal, Ph.D.

Sometimes the necessity to simulate rigid particles comes from the
existing FFs defining these nasty rigid particles, not from our own
desire to use them. So, it would be useful to get such feature in

Dr. Vitaly V. Chaban, Department of Chemistry
University of Rochester, Rochester, New York 14627-0216

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