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.abra...@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 > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >
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