AMBER Archive (2004)

Subject: AMBER: multiple heat bath GB+LES

From: Marcin Krol (mykrol_at_cyf-kr.edu.pl)
Date: Mon Jul 05 2004 - 11:53:31 CDT

Dear All,

I am trying to run MD simulations a protein-protein complex using GB+LES
and, as advised by prof. Simmerling, I am using two reference
temperatures for LES and non-LES systems.
Specifically, I set TEMP0LES to 150K and TEMP0 at
300K. First, I want to heat the system gently (I noticed form earlier
GB-non-LES runs that GB is very sensitive to the heating speed - if I heat
the system too quickly it is highly disrupted), so I use TAUTP = 10. This
works fine for GB-non-LES, but with LES I got LES-temp around 220K and not
165K I set. I assume that probably this is due to heat transfer from
non-LES to LES regions. In the production phase I use TAUTP=2.0 and I
T-LES oscilates around 170K which is better, but still not 150K I wnat it
to be. Therefore, the better idea would be to have two TAUTP, one for LES
(set to, say, 0.5) and the other for non-LES (set to 10 in the equil phase
and 2 in prod). Is it possible to specify two different TAUTP values?
Or maybe I can use ntt=3 for non-LES and ntt=1 for LES?

Thank you in advance
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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