[gmx-users] Pressure stabilization during NPT phase

[James Starlight]

This way I've already used but is this possible to extract Gro and trp
files from uncompleated runs and not stopping this simulation ?


James

2011/11/25 Mark Abraham <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>
>
>> 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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