AMBER Archive (2003)

Subject: Re: AMBER: SHAKE Problem

From: Xavier Periole (periole_at_sci.ccny.cuny.edu)
Date: Wed Aug 06 2003 - 15:26:05 CDT

Your volume has fluctuations (pretty high to my test) so you are in NPT !!
Probably not the problem but the heating process is generally done in
NVT. when you change your temperature the pressure changes and the
volume too. NOT good. Better NVT for heating, followed by equilibration
(of the water) and after you switch to NPT and equilibrate (the water)
again to get the right density and volume and ... equilibrated.

Can you have more information from your shake error. Because the sodium
is not supposed to get through shake: no bond to correct.

XAvier
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Xavier Periole, Ph.D.
Chemistry Dept.
City College of New York (CUNY)
138th St. and Couvent Av.
New York, NY 10010
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