Hello Prof. David, Kenneth,
Thanks for clearing that out. I started the simulation with parameters as
described by Prof. David. Actally I ran with thee parameters previously but
I am running after a long time hence I asked.Thanks for the response I will
still trap it.
Thanks again.
Regards,
SB
On Sat, Apr 25, 2015 at 4:05 PM, David A Case <case.biomaps.rutgers.edu>
wrote:
> On Sat, Apr 25, 2015, Soumendranath Bhakat wrote:
> >
> > Just a small query. I am planning to run two independent production run
> > from a equlibrated system (equi.rst file).
> >
> > I am setting up md.in with keywords irest=0 and ig=-1. Am I doing
> right? I
> > believe setting up irest=0 with ig==1 will start an independent
> simulation
> > from the last restart file (equil.rst).
>
> Probably the best is to set irest=0, tempi=300. (or whatever temperature
> you
> want), and ig=-1. This will randomize the velocities at the beginning of
> the
> run, and using ig=-1 will ensure that you have different random number
> schemes.
>
> >
> > Or if I only add irest=1 and ig=-1 then the ig=-1 will add random seed to
> > each simulation which will make them independent.
>
> This will also work: the random nature of the thermostat will quickly make
> the
> two trajectories independent. But it's easier to explain if you also
> completely randomize the velocities, as suggested in my first paragraph.
>
> ...dac
>
>
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--
Thanks & Regards;
Soumendranath Bhakat
Research Assistant, Division of Biophysical Chemistry, CMPS, Lund
University, Sweden
Homepgae: https://cbiores.wordpress.com/
Past: Molecular Modelling and Drug Design Research Group
Discipline of Pharmaceutical Sciences
UKZN, Westville
Weblink: http://soliman.ukzn.ac.za/Home.aspx
and Department of Pharmaceutical Sciences
Birla Institute of Technology, Mesra, India
in.linkedin.com/pub/soumendranath-bhakat/15/79b/b9/
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Received on Sun Apr 26 2015 - 08:00:03 PDT
