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On 15/06/2012 3:50 PM, James Starlight wrote:
<blockquote
cite="mid:CAALQopzwG34eG3r=S2dSbTzYY=-LQvB7o_mgzMBbJfd=vC0P5g@mail.gmail.com"
type="cite">Hi Tsjerk !<br>
<br>
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 ).<br>
</blockquote>
<br>
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 <a
href="http://www.gromacs.org/Documentation/How-tos/Reducing_Trajectory_Storage_Volume">http://www.gromacs.org/Documentation/How-tos/Reducing_Trajectory_Storage_Volume</a>
for some advice here.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAALQopzwG34eG3r=S2dSbTzYY=-LQvB7o_mgzMBbJfd=vC0P5g@mail.gmail.com"
type="cite">
<br>
<br>
James<br>
<br>
<div class="gmail_quote">2012/6/12 Tsjerk Wassenaar <span
dir="ltr"><<a moz-do-not-send="true"
href="mailto:tsjerkw@gmail.com" target="_blank">tsjerkw@gmail.com</a>></span><br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi James,<br>
<br>
Large-scale protein dynamics is low-frequency motion, so you
don't<br>
need a high time resolution. For large-scale dynamics alone,
something<br>
in the range of 1000-2500 frames should be sufficient,
depending on<br>
the size of the system. Note that larger systems require more
frames,<br>
as there will be more large scale dynamics to characterize.<br>
<br>
Cheers,<br>
<br>
Tsjerk<br>
<div class="HOEnZb">
<div class="h5"><br>
<br>
<br>
On Tue, Jun 12, 2012 at 9:29 AM, James Starlight <<a
moz-do-not-send="true"
href="mailto:jmsstarlight@gmail.com">jmsstarlight@gmail.com</a>>
wrote:<br>
> Mark,<br>
><br>
> Thanks for advise.<br>
><br>
> As I've found in that link the main way to reduce
dimension of the output<br>
> data is the ussage of appropriate nst* params in the
mdp file, exclusion of<br>
> the solvent from output and finally ussing compres
trajectories.<br>
><br>
> Could you tell me what are the most suitable size for
the nst* params for<br>
> the typical similation in water ( 50-250 ns) where I
want to observe both<br>
> large-scale protein dynamics as well locale
flexibility of the individual<br>
> side chain and solvent molecules ? Typically I've
used 5000 for evert nst*<br>
> params but that produce relatively big trajetories
even in the xtc format<br>
><br>
> James<br>
><br>
><br>
> 2012/6/12 Mark Abraham <<a moz-do-not-send="true"
href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>><br>
>><br>
>> On 12/06/2012 4:20 PM, James Starlight wrote:<br>
>>><br>
>>> Dear Gromacs Users!<br>
>>><br>
>>><br>
>>> I've forced with the problem during analysing
of long trajectories<br>
>>> consisted of > 5000 calculated for average
system ( ~ 35000 atoms). Commonly<br>
>>> I use VMD for analysing of such task but in
case of long trajectories<br>
>>> loading this software has been crashed with
the memory eror message. Could<br>
>>> you advise me the possible way to solve this
problem<br>
>><br>
>><br>
>> See<br>
>> <a moz-do-not-send="true"
href="http://www.gromacs.org/Documentation/How-tos/Reducing_Trajectory_Storage_Volume"
target="_blank">http://www.gromacs.org/Documentation/How-tos/Reducing_Trajectory_Storage_Volume</a><br>
>><br>
>><br>
>>> or another software for visualisation as well
as extraction of the<br>
>>> selected steps from trajectory as the pdb
files ?<br>
>><br>
>><br>
>> trjconv -h for command line cut'n'paste.<br>
>><br>
>> Insisting on doing analysis of data .pdb format
costs you time and space.<br>
>> If you're having problems with either, then you
should revisit whether you<br>
>> need that format.<br>
>><br>
>> Mark<br>
>> --<br>
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</div>
<span class="HOEnZb"><font color="#888888">--<br>
Tsjerk A. Wassenaar, Ph.D.<br>
<br>
post-doctoral researcher<br>
Molecular Dynamics Group<br>
* Groningen Institute for Biomolecular Research and
Biotechnology<br>
* Zernike Institute for Advanced Materials<br>
University of Groningen<br>
The Netherlands<br>
</font></span>
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