---------- Forwarded message ----------
From: Sajeewa Pemasinghe <sajeewasp.gmail.com>
Date: Fri, Jun 1, 2012 at 9:51 PM
Subject: Re: [AMBER] Fwd: problem with running equilibration MD in an LES
system
To: AMBER Mailing List <amber.ambermd.org>
First of all thank you very much for all your replies. As David had
mentioned I put ntr=1 and checked step by step what happens to temperature.
When the thermostat is there it actually starts at 300K then within about
100 steps (0.1ps) goes down to somewhere around 220K and then comes back to
300K and stays stable around 300K (within about 2-3ps). This has never
happened to me before (in non-LES systems, coz this is the first time I run
an LES system). This (starting at 300K,rapid decrease to somewhere around
220K, then increase to 300K gradually and staying around 300K with a little
bit of fluctuation)happens at each equilibration simulation (where I reduce
the force constant step by step). When I do my production MD in a Berendson
thermostat at 300K, the system starts at 300K, within 0.1ps goes down to
289K, within another 0.1ps comes back to 300K and stays around 300K. I
don't know if this kind of behavior is natural to LES systems or not. Your
advice is highly appreciated.
About ntx=7. I found that in Amber 11 ntx=7 is deprecated but is equivalent
to ntx=5. So I think whether I use ntx=7 or ntx=5, it will result in the
same output. Please correct me if I am wrong.
Thank you
Sajeewa Dewage
On Fri, Jun 1, 2012 at 6:51 PM, Brian Radak <radak004.umn.edu> wrote:
> Check your ntx option. I don't know what 7 does (it's not in the manual),
> but 5 is probably the one you want unless you are using binary restart
> files (are those in common use anymore?). If the velocities aren't read
> then temperature regulation will be reset so to speak and give rise to
> behavior as you described.
>
> Regards,
> Brian
>
> On Fri, Jun 1, 2012 at 11:42 AM, David A Case <case.biomaps.rutgers.edu
> >wrote:
>
> > On Fri, Jun 01, 2012, Sajeewa Pemasinghe wrote:
> > >
> > > The problem is the temperature at which the heating up ends is 300K. So
> > the
> > > next step should start at 300K and because I have used a heat bath,
> > should
> > > ideally stick around 300K. But what happens is that the next step
> > > (equilibration) starts at 200K
> >
> > Sounds like you have a problem that cannot be debugged remotely. Look
> > carefully at all the energies in the last step of the previous run and
> the
> > first step of the restart (using ntpr=1). Maybe that will help you hone
> > in on
> > what is happening. Double-check all your file names, and all the
> > parameters
> > in the mdin file, to make sure they are the same from one run to the
> next.
> >
> > ....dac
> >
> >
> > _______________________________________________
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> >
>
>
>
> --
> ================================ Current Address =======================
> Brian Radak : BioMaPS
> Institute for Quantitative Biology
> PhD candidate - York Research Group : Rutgers, The State
> University of New Jersey
> University of Minnesota - Twin Cities : Center for Integrative
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Received on Mon Jun 04 2012 - 09:30:02 PDT
