Hi Waad,
You may choose any number you like. This is the seed for the random
number generator used for the generation of the random force ...
The time of the RAMD simulations are system dependent and if you look at
the papers using the method you'll see that the time has increased from
the first paper (a couple of ps) significantly .. There is however no
rule about it .. You should just make sure that you do not 'destroy' the
protein in the simulation....
Of course, the longer the simulation the better (less perturbation) but
you also need to run different simulations with different parameters
and/or random number seeds ... Depending on the computer power you have
available you need a compromise between the length of a single
simulation and the number of different simulations
AMBER 8 is quite old already (and slow). If this is a limitation for
you, you may consider using the new RAMD version for NAMD.
http://projects.villa-bosch.de/mcm/software/namd/
Maybe at some point somebody will port the AMBER 8 patch to newer AMBER
versions.
Best
Vlad
Waad RHAIEM wrote:
>
>
> Dear amber users,
>
> I am trying to perform Random Acceleration Molecular Dynamics (RAMD)simulations
> using amber8 in order to explore exit trajectories of a ligand from its docking
> position in the buried active site of the enzyme. For this purpose, I would like
> to get further information about the time of RAMD simulations and about the
> parameter (iramdsd) which is the seed for the random number generator in RAMD
> simulations ( default value = 14253). Should I just choose different odd
> numbers or odd primes? small or large prime numbers and how large is large
> enough to get the best simulation (for example iramds = 100 vs iramdsd = 99999
> which the limit of iramdsd variable)
>
> thanks for any advice,
>
> Waad RHAIEM
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
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Dr. Vlad Cojocaru
Heidelberg Institute for Theoretical Studies
HITS gGmbH
Molecular and Cellular Modelling Group
Schloss-Wolfsbrunnenweg 35
69118 Heidelberg
Tel: ++49-6221-533202
Fax: ++49-6221-533298
e-mail:Vlad.Cojocaru[at]h-its.org
http://projects.villa-bosch.de/mcm/people/cojocaru/
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Received on Thu Apr 15 2010 - 01:30:02 PDT
