AMBER Archive (2005)

Subject: RE:AMBER: density problem

From: cristian obiol (c.obiol_at_qf.ub.es)
Date: Thu Jun 02 2005 - 03:14:21 CDT

Dear Shulin and Ross,

I understand that the way to solve the bubbles problem is :
1 - Run a short dynamics heat up ( i tried 0 to 120 K in 40ps)
2- Run a NPT dynamics to get the correct density (at 120 K)
3- Run again a dynamics to complete the temperature (120 to 300 K in 60ps)

Well, my problem continues because in the last step the bubbles appears again.

Best regards,

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

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