[gmx-users] Pressure stabilization during NPT phase

[Tsjerk Wassenaar]

Oh, I see I forgot to state that X should be set to the trajectory name:

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

or just

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

Cheers,

Tsjerk

On Fri, Nov 25, 2011 at 10:01 AM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
> 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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>>
>>
>>
>>
>>
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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
>



-- 
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