[gmx-users] Pressure stabilization during NPT phase

Mark Abraham 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 
perform well.


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