Hello,
I'm running a simulation to do GB implicit calculation of the free energy of hydration for a ligand. The simulation involves two md runs: one in vacuum and another in water. Then, four different "reprocessing" steps are executed. The free energy of hydration is obtained later using the BAR method. The md script that I use is below:
#!/bin/tcsh
sander -i water.in -p mol.prmtop -c mol.crd -o water.out -r water.rst -x water.c
rd -v water.vel -e water.ene -inf water.inf -O
sander -i vacuum.in -p mol.prmtop -c mol.crd -o vacuum.out -r vacuum.rst -x vacu
um.crd -v vacuum.vel -e vacuum.ene -inf vacuum.inf -O
#Do reprocessing
sander -i water_rerun.in -p mol.prmtop -c mol.crd -o water_water.out -r water_wa
ter.rst -y water.crd -v water_water.vel -e water_water.ene -inf water_water.inf
-O
sander -i vacuum_rerun.in -p mol.prmtop -c mol.crd -o water_vacuum.out -r water_
vacuum.rst -y water.crd -v water_vacuum.vel -e water_vacuum.ene -inf water_vacuu
m.inf -O
sander -i water_rerun.in -p mol.prmtop -c mol.crd -o vacuum_water.out -r vacuum_
water.rst -y vacuum.crd -v vacuum_water.vel -e vacuum_water.ene -inf vacuum_wate
r.inf -O
sander -i vacuum_rerun.in -p mol.prmtop -c mol.crd -o vacuum_vacuum.out -r vacuu
m_vacuum.rst -y vacuum.crd -v vacuum_vacuum.vel -e vacuum_vacuum.ene -inf vacuum
_vacuum.inf -O
I'm n ot sure what the reprocessing steps do. It is clear they take as input the trajectories generated in the first two steps (vacuum.crd and water.crd). As examples, I include the input files vacuum.in and vacuum_rerun.in:
vacuum.in:
trajectory segment
&cntrl
imin = 0, nstlim = 5000000, ntwr = 5000,
nscm=100,
igb = 0, gbsa = 0,
cut=24.0,
tempi = 300, ntt = 3, temp0 = 300,
ntpr=5000,
gamma_ln=1,
vlimit = 0.000,
ntc=2, ntf = 2, tol = 1.0d-8
dt = 0.002, nrespa = 2,
ntb = 0, ntave = 0,
ioutfm = 0, ntwx = 5000, ntwe = 5000,
ntr = 0,
ig=27145
&end
END
END
vacuum_rerun.in:
trajectory segment
&cntrl
imin = 5, maxcyc = 1, nstlim = 5000000, ntwr = 5000,
nscm=100,
igb = 0, gbsa = 0,
cut=24.0,
tempi = 300, ntt = 3, temp0 = 300,
ntpr=5000,
gamma_ln=1,
vlimit = 0.000,
ntc=2, ntf = 2, tol = 1.0d-8
dt = 0.002, nrespa = 1,
ntb = 0, ntave = 0,
ioutfm = 0, ntwx = 5000, ntwe = 5000,
ntr = 0,
ig=27145
&end
END
The only difference between vacuum.in and vacuum_rerun.in is that in the latter:
imin=5, maxcyc=1, nrespa=2
while imin=0, nrespa=1 in the former.
Thanks for the help.
Khaled
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Received on Wed Feb 08 2012 - 04:30:03 PST
