I can't say for sure, but it surprises me that dropping the T would cause
problems. You might want to vary things and check. for example, does the
rapid drop cause Inf energies when you don't turn on the restraints? does
it matter if the structure is already well equilibrated? does it happen
when you don't have any non-standard residues (could be a force field
problem, not the thermostat).
On Wed, Aug 31, 2016 at 6:33 AM, Thomas Evangelidis <tevang3.gmail.com>
wrote:
> Thanks Carlos!
>
> Is this intermediate annealing from 290->50 K necessary? I want to run many
> simulations like this and want to save time if possible. In my experience
> with 2 separate simulations with the restraints shown in my script, the
> chances of getting inf energies after restarting the 290 K simulation at 50
> K are higher when using igb=7 rather than igb=1 for example.
>
> On 31 August 2016 at 02:19, Carlos Simmerling <carlos.simmerling.gmail.com
> >
> wrote:
>
> > The weight changes aren't read unless you set nmropt.
> >
> > On Aug 30, 2016 7:51 PM, "Thomas Evangelidis" <tevang3.gmail.com> wrote:
> >
> > > Greetings,
> > >
> > > I am trying to equilibrate my system at 290 K, then drop gradually the
> > > temperature to 50 K and do a small production MD. At the beginning I
> did
> > it
> > > using two simulations with 2 individual input files, namely by skipping
> > the
> > > gradual lowering of the temperature from 290 to 50 K. However, at 30%
> of
> > > the times the 2nd simulation at 50 K had infinite energies. My
> conclusion
> > > was that this was due to the restraints I was applying. So I decided to
> > add
> > > this intermediate step that lowers gradually the temperature all in one
> > > script this time. A sample AMBER input looks like this:
> > >
> > > &cntrl
> > > > nstlim=10000, cut=999, igb=1, saltcon=0.2, gbsa=0,
> > > > ntpr=100, ntwr=500, ntt=3, gamma_ln=10.0,
> > > > ntx=1, irest=0, ntp=0,
> > > > ntc=2, ntf=2, tol=0.000001,
> > > > dt=0.002, ntb=0, ig=-1,
> > > > ioutfm=1, ntxo=2, ntwx=500,
> > > > ntr=1, ntrx=1, restraint_wt=100,
> > > > restraintmask="! ( (:LIG <:5) &! (.CA,C,O,N,H) | :LIG )",
> > > > &end
> > > > &wt type='TEMP0', istep1=0,istep2=5000,value1=290.,value2=290., &end
> > > > &wt type='TEMP0', istep1=5001,istep2=7500,value1=290.,value2=50.,
> &end
> > > > &wt type='TEMP0', istep1=7501,istep2=10000,value1=50.,value2=50.,
> &end
> > > > &wt type='END', &end
> > >
> > >
> > > The problem is that the temperature remains at 290-300 K throughout the
> > > 10,000 steps of the simulation. Could someone please troubleshoot me?
> > >
> > > thanks,
> > > Thomas
> > >
> > > --
> > >
> > > ======================================================================
> > >
> > > Thomas Evangelidis
> > >
> > > Research Specialist
> > > CEITEC - Central European Institute of Technology
> > > Masaryk University
> > > Kamenice 5/A35/1S081,
> > > 62500 Brno, Czech Republic
> > >
> > > email: tevang.pharm.uoa.gr
> > >
> > > tevang3.gmail.com
> > >
> > >
> > > website: https://sites.google.com/site/thomasevangelidishomepage/
> > > _______________________________________________
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> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
>
> ======================================================================
>
> Thomas Evangelidis
>
> Research Specialist
> CEITEC - Central European Institute of Technology
> Masaryk University
> Kamenice 5/A35/1S081,
> 62500 Brno, Czech Republic
>
> email: tevang.pharm.uoa.gr
>
> tevang3.gmail.com
>
>
> website: https://sites.google.com/site/thomasevangelidishomepage/
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Received on Wed Aug 31 2016 - 04:30:02 PDT
