AMBER Archive (2002)

Subject: example gibbs file for the methane tutorial

From: Andreas Kerzmann (anker_at_bioinf.uni-sb.de)
Date: Fri Aug 30 2002 - 05:18:06 CDT

Hi all,

if anyone is interested in a hopefully correct translation of the
gibbs_simple.interf file from the methane tutorial to a regular gibbs input
file, have a look at the end of this mail. Probably somebody already posted
this to the list, but I didn't find anything. Maybe someone finds this
useful.

But I'm curious: Why was the interface code dropped in release 7?

Cheers,

  Andreas Kerzmann

Version 1:

----- cut here -----
 simple gibbs free energy calculation (taken from the mathane tutorial)
 &cntrl
# read amber formatted x, v and box values
        NTX = 7,
# time Limit
        TIMLIM = 99999999.0,
# starting temperature
        TEMP0 = 300.0,
# target temperature
        TEMPI = 300.0,
# split temperature scaling for solute and solvent using Berendsen
        NTT = 5,
# tempersture relaxation time for the solute
        TAUTS = 0.20,
# limit velocity
        VLIMIT = 10.0,
# periodic boundary with constant pressure dynamics
        NTB = 2,
        NTP = 1,
# calculate ALL solute-solute nonbonded interactions
        IFTRES = 0,
# temperature relaxation time
        TAUTP = 0.6,
# reference pressure
        PRES0 = 1.0,
# the timestep
        DT = 0.001,
# update
        NSNB = 25,
# cutoff
        CUT = 8.0,
# constant dielectric
        IDIEL = 1,
# shake all bonds
        NTC = 3,
# relative tolerance for bond constraints
        TOL = 0.00000001,
# retry
        ISHKFL = 5,
# control mixed vdW-parameters of vanishing atoms
        IDSX0 = 400,
# intraperturbed group energies
        INTPRT = 5,
# calculate entropies
        ISANDE = 1,
# d_TEMP.
        DTUSE = 0.5,
# run every MD sim for 20000 steps
        NSTLIM = 20000,
# number of runs
        NRUN = 21,
# report free energies every 20000 steps
        NTATDP = 20000,
# starting with lambda = 1.0
        ALMDA = 1.0,
# window width
        ALMDEL = 0.05,
# equilibrate 5000 steps in each window
        NSTMEQ = 5000,
# collect data every 15000 steps
        NSTMUL = 15000,
# perturb to 0.0 with fixed width lambda intervals
        ISLDYN = -3,
# use thermodynamic integration
        IDIFRG = 1,
# missing in interface script
        SCEE = 1.2,
 &end
----- cut here -----

Version 2:
(created from Version by applying "grep -v \# gibbs1.in.commented > gibbs1.in")

----- cut here -----
 simple gibbs free energy calculation (taken from the mathane tutorial)
 &cntrl
        NTX = 7,
        TIMLIM = 99999999.0,
        TEMP0 = 300.0,
        TEMPI = 300.0,
        NTT = 5,
        TAUTS = 0.20,
        VLIMIT = 10.0,
        NTB = 2,
        NTP = 1,
        IFTRES = 0,
        TAUTP = 0.6,
        PRES0 = 1.0,
        DT = 0.001,
        NSNB = 25,
        CUT = 8.0,
        IDIEL = 1,
        NTC = 3,
        TOL = 0.00000001,
        ISHKFL = 5,
        IDSX0 = 400,
        INTPRT = 5,
        ISANDE = 1,
        DTUSE = 0.5,
        NSTLIM = 20000,
        NRUN = 21,
        NTATDP = 20000,
        ALMDA = 1.0,
        ALMDEL = 0.05,
        NSTMEQ = 5000,
        NSTMUL = 15000,
        ISLDYN = -3,
        IDIFRG = 1,
        SCEE = 1.2,
 &end
----- cut here ----- 

-- 
Andreas Kerzmann                                      phone +49-681-302-64709
Center for Bioinformatics                               fax +49-681-302-64719
anker_at_bioinf.uni-sb.de                                 http://www.cbi-saar.de