From: ben estimated.com (ben_at_estimated.com)
Date: Sun Jan 26 2020 - 22:07:34 CST
I'm heating my system from 200K to 310K by coupling a heat bath to the only the solvent atoms. I did this by using NAMD's "tCouple" and setting the B value of all the water molecules in the PDB file to 1. I am also using a 2fs timestep and therefore have rigidbonds to "all." If the water molecules are unable to vibrate/stretch because of this, does it still make sense to heat them and expect my simulation to be physiologically realistic? (I assume this problem would still exist even if I set rigidbonds to "water").
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