I am looking for certain structural features in globular proteins. I have to perform an MD simulation of a distorted structure (with certain native features and many steric clash) with constraints imposed on the main-chain dihedral angles (in CHARMM). Before the MD, I have to do a minimization where I see the structure getting swelled severely in order to release the clashes. Is there a way to impose another constraint in volume?
In charmm you can also do position restraints using "cons harm", which does not allow large motions of atoms. You can also look at "cons drop", at least from the documentation may be used to constrain the volume of the molecule. The online documentation of how to use them is given in the following link:
http://www.charmm.org/documentation/c38b1/cons.html
Dear Hiqmet, Many thanks, I have already used 'cons harm' .. checking for 'cons drop'
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