AMBER Archive (2005)

Subject: RE:AMBER: density problem

From: cristian obiol (c.obiol_at_qf.ub.es)
Date: Wed Jun 08 2005 - 03:56:23 CDT

Dear AMBER users,

In my previous message I still had the bubbles in the water box.
After testing some methods (thanks for the help) to enlarge the density, I
have been able to solve the problem with a little anisotropic pressure NTP=2
step (only to the box) after the normal heat step to 300K. Then, the density
enlarged to 0.99 in a very fast way and the bubbles dissapeared.
I'm not sure if this NTP=2 step is correct in protein complexes but it runs !

Regards,

Cristian Obiol
Biological Systems Modelling
and Drug Design Research Group
University of Barcelona

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