Fwd: Running a simulation with coarse-grained protein in membrane

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.
francesco

---------- 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>

HI:
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.

francesco pietra

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 05:22:35 CST