AMBER Archive (2002)

Subject: Is H-bonding really there?

From: suvendu lomash (suvendu_lomash_at_yahoo.com)
Date: Fri Sep 27 2002 - 14:59:48 CDT

HI !!
I 've been equilibriating water in a solvated box
using the gradual warming approach. I don't have any
problems as such - just a thought here. I get the
impression from MD output files that AMBER can
simulate H-bonding. If this is true, then during my
gradual warming of the solvated box I should not get
any velocity of water molecules till I cross the
temprature of 273K because they should be in a rigid
3d cage structure (ice). why is there this apparent
paradox?
thanks.
Suvendu.

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