On 25/11/2011 5:22 PM, James Starlight wrote:
Dear Gromacs Users!
At the present time I'm simulating small peptide (11 a.c in coiled
conformation) in water.
I've desided to use parameters from Lysozyme simmulation ( opls ff for
parametrisation and all mdp parameters from that simulation).
Because my peptide was smaller than typical globular protein I've
desided to use bigger periodical box than in tutorial
I've used editconf -c -d 1.5 -bt cubic instead of 1.0 nm in tutorial
wich resulted in bigger box relative peptide size.
so i have this box vectors 5.39318 5.39318 5.39318
My experiment was in full agreement with the above tutorial until NVP
phase was conducted. I have conducted 100ps equilibration but When
I've checked average pressure it was 0.75 atm instead of 1 BAR and
have big RMSD- 200. (also I've checked my system visually but it looks
fine- I have not pointed any artifacts linked with unstable pressure
like voids in the solvent etc).
Seems normal for a tiny simulation -
http://www.gromacs.org/Documentation/Terminology/Pressure
Should I equilibrate my sustem longer until pressure would not be
stabilized to reference BAR? What another options should i take into
account during simulation of the small peptides ?
Seek to reproduce conditions that other published studies have shown
perform well.
Mark
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