Hi,
Yes the restart file is from an MD run of the same system. What I am doing
is
1) Placing 50 copies (initiallly 100 and then reduced to 50) of ammonia at
a particular position in the protein using addles
2) Neutralizing and then minimizing the system
3)Heating up to 300K in 10ps (50 kcalmol-1A-2 force constant with shake)
4)Removing the constraints step by step in 20ps
5)Running unconstrained production MD for 200ps
At each step the restart file of the previous step is used. In the heating
up the temperature goes up as expected. Then when I use the restart file
generated at the end of the heating up step (which has a force constant of
50 kcalmol-1A-2) and use it to run MD in NVT ensemble using a Berendson
thermostat (I tried Langevin as well, separately but with the same result)
the system temperature behaves as I described earlier. I have run Non-LES
MD with the same conditions before (with shake) but this kind of ups and
downs in temperature were not seen.
Thank you
Sajeewa
On Mon, Jun 4, 2012 at 12:44 PM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> I haven't been following this in detail and am not sure if you changed
> anything in your inputs, but it's possible that if you use shake that
> the initial temperature drops as shake removes velocities along the
> bonds. then it goes back up with the thermostat. to know if this is
> what's going on you'd need to explain in detail where the input
> restart file came from- was it an MD run of exactly the same system,
> the same prmtop, etc? exactly what changed between the previous run
> and this one?
>
> On Mon, Jun 4, 2012 at 12:25 PM, Sajeewa Pemasinghe <sajeewasp.gmail.com>
> wrote:
> > ---------- 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
> >> Proteomics Room 308
> >> Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
> >> Department of Chemistry : Piscataway, NJ
> >> 08854-8066
> >> radak004.umn.edu :
> >> radakb.biomaps.rutgers.edu
> >> ====================================================================
> >> Sorry for the multiple e-mail addresses, just use the institute
> appropriate
> >> address.
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Received on Mon Jun 04 2012 - 10:30:03 PDT
