[gmx-users] Pressure stabilization during NPT phase
Mark.Abraham at anu.edu.au
Fri Nov 25 08:01:32 CET 2011
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 -
> 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
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