AMBER Archive (2007)

Subject: AMBER: Squished dimer during transition from NVT to NPT

From: Katrina Lexa (klexa_at_umich.edu)
Date: Thu Aug 30 2007 - 16:02:20 CDT

Hello AMBER users.
In the explicitly solvated system that I'm working with, as I change the
settings from NVT to NPT and the box is resized, my dimer is obviously
considered as two separate molecules in my system and so when the volume
of the box changes, so does the distance between my two dimers. At this
point in the simulation, only the solvent is being equilibrated at final
temperature and the dimer is restrained. I've also tried actually
freezing it in place, but the two monomers still shift as separate
entities according separate centers of mass. Since having my two
monomers crash together isn't particularly helpful for my research, I am
hoping someone might know how I could prevent this from occurring.
Thank you,
Katrina

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