AMBER Archive (2002)

Subject: Re: input files

From: Carlos Simmerling (carlos.simmerling_at_sunysb.edu)
Date: Wed Apr 03 2002 - 07:40:30 CST

Monica,
here is a simple annealing using GB solvation.
It heats from 300K to 500K, holds at 500K then cools to 0K.
It is a simple example to show the input, and
is probably too short to be useful.
Carlos

heat system to 500K over 5ps, hold at 500K for 5ps then cool to 0K over 10ps
 &cntrl
     imin = 0, ntx = 1, nstlim = 2000,
     temp0 = 300.0, tempi = 300.0, igb = 1,
     ntt = 1, dt = 0.001, tol=0.000001,
     ntc=2, ntf=2, ntb=0, tautp=0.01,
     ntcm=1, nscm=10000,
     ntwx = 100, ntwe = 0, ntwr = 1000, ntpr = 100,
     scee = 1.2, cut = 100.0,
     nmropt=1,
 &end
 &wt
        TYPE='TEMP0', istep1 = 1, istep2 = 500,
        value1 = 300, value2 = 500,
 &end
 &wt
        TYPE='TEMP0', istep1 = 501, istep2 = 1000,
        value1 = 500, value2 = 500,
 &end
 &wt
        TYPE='TEMP0', istep1 = 1001, istep2 = 2000,
        value1 = 500, value2 = 0,
 &end
 &wt
   type="END",
 &end
 &rst
   iat(1)=0,
 &end

----- Original Message -----
From: "Monica" <monicdbs_at_iitr.ernet.in>
To: "AMBER" <amber_at_heimdal.compchem.ucsf.edu>
Sent: Wednesday, April 03, 2002 8:00 AM
Subject: input files

>
> Hello to all,
> can anyone send me his input file for simulated annealing. I am working
> on DNA hexamer.I just want to see how various inputs are given.
> I will be very grateful to you.
> thanks
> Monica
> Deptt Biosci Biotech
> IIT,Roorkee
> Roorkee-247667
> Uttranchal
>
>