Running a simulation with coarse-grained protein in membrane

From: Francesco Pietra (francesco.pietra_at_accademialucchese.it)
Date: Mon Dec 07 2009 - 12:36:16 CST

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

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