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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>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>>
>>
>>
>> --
>> ================================ 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 - 10:00:03 PDT
