From: Mallajosyula, Sairam (smallajo_at_rx.umaryland.edu)
Date: Thu Jan 05 2012 - 21:41:05 CST
Is it possible to simulate TIP5P water using NAMD. I have successfully run this using CHARMM, but due to the system
size i want to use NAMD. Here are my observations.
1) NAMD does not recognize the lone pairs in TIP5P water model. This is evident from the following message
Warning: FOUND 16764 ATOMS WITH ZERO OR NEGATIVE MASSES! CHANGED TO 0.001
As a test i used the TIP4 water model and found that it recognized the lone pair.
Warning: CORRECTION OF ZERO MASS ATOMS TURNED OFF BECAUSE LONE PAIRS ARE USED
*** So is there a key word which enables lone pair recognition.
2) NAMD gives me the following error
ERROR: Atom 484 velocity is 10430.7 -5415.58 -3101.58 (limit is 12000)
It is obvious that this is due to the mass less lone pairs.
On searching the namd list i did not find many insights into this. There have been suggestions on imposing
large force constants. But i do not know is this is the best way to go about it.
I would appreciate some insights into this issue.
Dr. Sairam S. Mallajosyula
Computer Aided Drug Design Center
University of Maryland
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