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
http://www.cbi-saar.de
Received on Fri Aug 30 2002 - 03:18:06 PDT
