[gmx-users] analysing of the long trajectories

[Mark Abraham]

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