[gmx-users] Pressure stabilization during NPT phase

Tsjerk Wassenaar tsjerkw at gmail.com
Fri Nov 25 10:01:41 CET 2011


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



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