[gmx-users] analysing of the long trajectories

[Mark Abraham]

On 15/06/2012 3:50 PM, James Starlight wrote:
> 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 ).

nst* are numbers of steps between events. If you want finer time 
resolution to see events on short time scales, you need *smaller* values 
for these, and talking about the number of steps is meaningless unless 
you state the size of the time step. See 
http://www.gromacs.org/Documentation/How-tos/Reducing_Trajectory_Storage_Volume 
for some advice here.

Mark

>
>
> James
>
> 2012/6/12 Tsjerk Wassenaar <tsjerkw at gmail.com <mailto: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 <mailto: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
>     <mailto: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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>
>     --
>     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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