[gmx-users] analysing of the long trajectories

[Tsjerk Wassenaar]

Hi James,

Large-scale protein dynamics is low-frequency motion, so you don't
need a high time resolution. For large-scale dynamics alone, something
in the range of 1000-2500 frames should be sufficient, depending on
the size of the system. Note that larger systems require more frames,
as there will be more large scale dynamics to characterize.

Cheers,

Tsjerk



On Tue, Jun 12, 2012 at 9:29 AM, James Starlight <jmsstarlight at gmail.com> wrote:
> Mark,
>
> Thanks for advise.
>
> As I've found in that link the main way to reduce dimension of the output
> data is the ussage of appropriate nst* params in the mdp file, exclusion of
> the solvent from output and finally ussing compres trajectories.
>
> Could you tell me what are the most suitable size for the nst* params for
> the typical similation in water ( 50-250 ns) where I want to observe both
> large-scale protein dynamics as well locale flexibility of the individual
> side chain and solvent molecules ? Typically I've used 5000 for evert nst*
> params but that produce relatively big trajetories even in the xtc format
>
> James
>
>
> 2012/6/12 Mark Abraham <Mark.Abraham at anu.edu.au>
>>
>> On 12/06/2012 4:20 PM, James Starlight wrote:
>>>
>>> Dear Gromacs Users!
>>>
>>>
>>> I've forced with the problem during analysing of long trajectories
>>> consisted of > 5000 calculated for average system ( ~ 35000 atoms). Commonly
>>> I use VMD for analysing of such task but in case of long trajectories
>>> loading this software has been crashed with the memory eror message. Could
>>> you advise me the possible way to solve this problem
>>
>>
>> See
>> http://www.gromacs.org/Documentation/How-tos/Reducing_Trajectory_Storage_Volume
>>
>>
>>> or another software for visualisation as well as extraction of the
>>> selected steps from trajectory as the pdb files ?
>>
>>
>> trjconv -h for command line cut'n'paste.
>>
>> Insisting on doing analysis of data .pdb format costs you time and space.
>> If you're having problems with either, then you should revisit whether you
>> need that format.
>>
>> Mark
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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