[gmx-users] Pressure stabilization during NPT phase

[Mark Abraham]

On 25/11/2011 6:38 PM, James Starlight wrote:
> 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)  ?

Choose a length of time in advance that you are happy to risk being 
wasted. Run that length of time, make a backup, check whatever you want 
to check, then continue the simulation. As you acquire confidence, you 
will want to increase that time (and like everyone you will regret that 
decision at least once!)

Mark

>
>
>
> Thanks again
>
> James
>
> 2011/11/25 Tsjerk Wassenaar <tsjerkw at gmail.com <mailto: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 <mailto: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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