[gmx-users] Pressure stabilization during NPT phase

Tsjerk Wassenaar tsjerkw at gmail.com
Fri Nov 25 08:04:04 CET 2011

Hi James,

There have been extensive discussions about this on the list. Check the
archives. In short, smaller systems give larger fluctuations, and shorter
simulations give larger deviations from the expected average.



On Nov 25, 2011 7:23 AM, "James Starlight" <jmsstarlight at gmail.com> 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). 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 ?



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