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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> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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>
--
======================================================================
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 - 04:00:02 PDT
