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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Received on Tue Aug 30 2016 - 17:30:03 PDT
