> I am currently equilibrating a system for MD like many times before. The problem
> is that during the NTP pressure adjustment step my complex gets distorted. This
> is due to the distance rescaling. It has not been a big deal for globular
> proteins with the ligand rather close to the center of the solvent box since the
> rearrangement of the complex was minimal.
The easiest way is to hack the prmtop to trick the system to think that
all the atoms in your complex are in a single molecule and to apply
molecule based pressure scaling. The less easy way is to modify the code
to avoid scaling of the restraint coordinates at each step. A third
option is to not apply positional restraints (instead use distance
restraints, however you'd have to create up a list of these or obtain from
NMR data).
To hack the prmtop, see: http://ambermd.org/Questions/mail/303.html
-tec3
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Received on Fri Sep 10 2010 - 17:30:05 PDT
