[gmx-users] analysing of the long trajectories

[James Starlight]

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 <tsjerkw at 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 <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
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