[gmx-users] Running MD only for selected part of molecule

Erik Lindahl lindahl at cbr.su.se
Sun Oct 12 14:18:26 CEST 2008


On Oct 10, 2008, at 12:46 PM, Justin A. Lemkul wrote:
>> I want to run MD over a part of my molecule , for few residues only  
>> (not the whole molecule).
>> Can I do it using GROMACS ?
>> I searched for the online documentation and mailing list, but  
>> unable to get appropriate information.
>> If somebody has already tried such things earlier, please suggest  
>> and direct me for appropriate link and address.
> Well, if your goal is to keep certain parts fixed and allow others  
> to move, probably the easiest way to do it is to apply position  
> restraints to the "fixed" part.

You can also set parts of the system as a freeze group, in which case  
you can exclude all nonbonded interactions inside the freeze group  
with the energygrp_excl option in your mdp file.

The main advantage of this is of course that you will improve  
performance if 99% of your system is frozen (although all interactions  
between the frozen and non-frozen parts still have to be calculated).  
On the other hand, completely freezing part of the system is not very  
realistic, and you're likely to get strange behavior in the interface...



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