Hi Tsjerk ! I my case I want to compare large-scale dynamics with more local events like fluctuation of the individual side chains so I suppose that I need larger number of frames. But how exactly I could define this number for my 100ns trajectory? Commoly I've used 5000 value for all nst* options in MDP file but that produce trajectories with ~ 10.000 frames for 100ns. If I increase this values from 5000 to 10000 could I see dynamics on the level of the individual side-chains ? ( e.g occurence of salt-bridges or rotamer isomerisation of the polar side chains during my 100ns trajectory ).
James 2012/6/12 Tsjerk Wassenaar <tsje...@gmail.com> > 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 <jmsstarli...@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.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 > >> > >> > >>> 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 > >> Please search the archive at > >> 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 > > > > > > > > -- > > gmx-users mailing list gmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at > > 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 > > > > -- > 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 > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > 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 >
-- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at 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