From: Mariana Graterol (marianagraterol_at_gmail.com)
Date: Thu Sep 27 2012 - 08:35:31 CDT
Dear NAMD users:
I'm trying to balance my protein in a water box using periodic conditions;
initially had a very low density (0.85 g / ml) and in the first run at 300
K, many bubbles were formed.
Then, I change the size of the box and prepared so that the density was
1.00 g/ml. Anyway, the first thing I did with my system was minimized and
then perform the heating, if I heat the system in NPT ensemble, the volume
increases initially, to leave me with a low density 0.87 g/ml. I've seen
many posts on the list, articles, etc... that equilibration protocols using
Langevin thermostat and barostat is reached at 300 K and 1 atm, in that
first run, setting the volume to its proper value, not increasing it.
It does not seem appropriate behavior, since, the equilibrium stage should
be to set the initial system and bring it to reality, convergent values
in terms of temperature, pressure and density. But in my case, I do not
see this.
Furthermore, if I heat at constant volume (NVT), is greatly increased
pressure (1000-1300 bar) and then the piston appears not to work and the
pressure is regulated only at the expense of an increase in volume.
Some might recommend a protocol for TP-volume set initially?
I am using a restriction backbone atoms (not H) of my protein (K= 1500
Kcal/mol.AA2) and some of the parameters show below:
Thanks a lot,
cutoff 12.000000
switching on
switchdist 10.000000
pairlistdist 14.000000
# Periodic boundary conditions
cellBasisVector1 109 0.000000 0.000000
cellBasisVector2 0.000000 111 0.000000
cellBasisVector3 0.000000 0.000000 86
cellOrigin 0.000001 0.000000 0.000000
# Harmonic constraints
constraints on
consexp 2
conskcol B (K= 1500 Kcal/mol. AA2)
constraintScaling 1.000000
conskfile C:\\Users\\pc\\Documents\\cal\\estructure.pdb
consref C:\\Users\\pc\\Documents\\cal\\estructure.pdb
# Langevin dynamics
langevin on
langevinTemp 300.000000
langevinHydrogen off
langevinDamping 5.000 (1/ps)
# Constant pressure control
langevinPiston on
langevinPistonTarget 1.01325 (bar)
langevinPistonPeriod 1000 (fs)
langevinPistonDecay 500 (fs)
langevinPistonTemp 300 (K)
-- * mari *
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