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 <tsje...@gmail.com <mailto: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 <mailto: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
<mailto: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
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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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