AMBER Archive (2004)

Subject: AMBER: GB+LES

From: Marcin Krol (mykrol_at_cyf-kr.edu.pl)
Date: Wed Jun 30 2004 - 04:43:27 CDT

Dear All

I would liketo run LES+GB simulations to quickly sample side chain
coformations. I am, however, confused by the omas keyword. I think I
should not use this keyword and scale masses of LES atoms by 1/NC to get
corect thermal energy. On the other hand all examples in the manual
include omas keyword. When I run LES MD with omas I got highly distorted
structure in the area where LES copies where. Without omas I often get
shake error. Could you please comment/give advice on the use of omas
keyword (scaling of masses).

Thank you in advance for your answer

Best regards
marcin

Dr Marcin Krol
Zaklad Bioinformatyki Collegium Medicum UJ
Kopernika 7E
31-501 Krakow
tel/fax (012) 422-77-64
e-mail mykrol_at_cyf-kr.edu.pl
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