[gmx-users] Pressure stabilization during NPT phase

[Tsjerk Wassenaar]

Hey,

You don't actually need to copy the trajectory. trjconv and other
tools are comfortable operating on an unfinished trajectory. They'll
just bail out at the end. As an alternative, here's a python one-liner
to extract the last frame (along with unfinished frames) from an XTC
trajectory:

python -c 'X=open("'$X'").read(); print X[X.rfind(X[:8]):]' > last.xtc

It will read in the whole trajectory in memory, so better not do it
with very large files ;)

Cheers,

Tsjerk

On Fri, Nov 25, 2011 at 9:08 AM, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> 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>
>>
>> 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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>>
>>
>>
>>
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands