Namd list: Problem in equilibration stage

From: Mariana Graterol (
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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