[gmx-users] Pressure stabilization during NPT phase

[James Starlight]

Mark, Tsjerk thanks!

I've check my uncompleated produced MD run by G_energy and find that
average pressure is 1.1 Bar that is most close to ref.


By the way could you tell me about extra possible ways of checking running
simmulation? ( E.g I'm calculating long produce trajectory and want to
check my uncompleated system ).

As I understood One of the possible way is the ussage of G_energy but how I
could obtain GRO and TPR file from uncompleated MD trajectory ( .trr)
(recently I've asked about this but I've missed that topic ;o)  ?



Thanks again

James

2011/11/25 Tsjerk Wassenaar <tsjerkw at gmail.com>

> 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.
>
> Cheers,
>
> Tsjerk
>
> 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 ?
>
> Thanks,
>
> James
>
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