[AMBER] lowering the temperature

From: Thomas Evangelidis <tevang3.gmail.com>
Date: Wed, 31 Aug 2016 01:51:40 +0200


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:

> 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?


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
website: https://sites.google.com/site/thomasevangelidishomepage/
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Received on Tue Aug 30 2016 - 17:00:02 PDT
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