[gmx-users] analysing of the long trajectories

[James Starlight]

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<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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