[gmx-users] Pressure stabilization during NPT phase

[Mark Abraham]

On 25/11/2011 6:53 PM, James Starlight wrote:
> This way I've already used but is this possible to extract Gro and trp 
> files from uncompleated runs and not stopping this simulation ?

Copy the trajectory file. Then use trjconv on the copy however suits 
you. You don't need a new .tpr, you need either the original .tpr or one 
that suits your analysis.

Mark

>
>
> James
>
> 2011/11/25 Mark Abraham <Mark.Abraham at anu.edu.au 
> <mailto:Mark.Abraham at anu.edu.au>>
>
>     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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