From: Francesco Pietra (francesco.pietra_at_accademialucchese.it)
Date: Tue Dec 08 2009 - 09:54:46 CST
Please, only retain "Has any adaptation [of membrane tutorial] to CG
already been posted beyond setting a much larger time step?" from my
original message. All other is clear from the tutorial, which I would
have studied before posting.
---------- Forwarded message ----------
From: Francesco Pietra <francesco.pietra_at_accademialucchese.it>
Date: Mon, Dec 7, 2009 at 7:36 PM
Subject: Running a simulation with coarse-grained protein in membrane
To: NAMD <namd-l_at_ks.uiuc.edu>
New to namd, with Amber experience, I want to perform md with a
water-solvated protein in popc membrane (all coarse-grained, CG). I am
following the guidelines of the August 2009 membrane-protein tutorial
from namd tutorials. Having already setup the system with VMD and
other software, I start from section "3.2 Minimization and
Equilibration with Protein Constrained".
Has any adaptation to CG already been posted beyond setting a much
larger time step? If I understand the sample configuration file for
minimization-equilibration, why 300K and constant pressure? I expected
minimization at constant volume and 0K, then gradually bringing the
system to room temp.
Thanks for any input to put me on the way.
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