Hi, All,
I calculated the free energy difference of H3C-OH and H3C-SH in VACUUM, with the following script (modificated from Dr. Case's). But the results were strange. When clambda near zero, the values of dV/dl were really large, as shown by the fig in attachment. Obviously, the final result was far from convergence. Is there something wrong with my input, or something else?
Also, I did the same thing with gibbs with the same perturbed .prmtop file, the input file was come from here,
http://web.njit.edu/all_topics/Prog_Lang_Docs/html/amber7/crown_ether/pert/gib10.in
This time, I got a "reasonable" result: F_energy=-1.88804. Is it really reasonable?
Attachment is the figure and the perturbed .prmptop file.
Thanks a lot in advance!
________________________________________________________________________________
#! /usr/bin/perl -w
foreach $in ( 0 .. 40 ){
$clambda = 0.025*$in;
$out = $in + 1;
## equilibration:
open( MDIN, ">mdin");
print MDIN <<EOF;
CYS to SER in-vacuo, no cut off
&cntrl
imin = 0, ntb = 0, nscm =50 ,
irest = 1, ntx = 5,
igb = 0, ntpr = 100, ntwx = 0,
ntt = 1,
tempi = 300.0, temp0 = 300.0,
nstlim = 100000, dt = 0.002,
icfe=1, clambda=$clambda, klambda=6,
cut = 999.
/
EOF
close MDIN;
system(" /home/tan/amber8/exe/sander -O -i mdin -p cys_ser.prmtop -c cys_ser$in.rst -r cys_ser$out.erst");
## production:
open( MDIN, ">mdin");
print MDIN <<EOF;
CYS to SER in- vacuo, no cut off
&cntrl
imin = 0, ntb = 0, nscm =100 ,
irest = 1, ntx = 5,
igb = 0, ntpr = 100, ntwx = 0,
ntt = 0,
tempi = 300.0, temp0 = 300.0,
nstlim = 100000, dt = 0.002,
icfe=1, clambda=$clambda, klambda=6,
cut = 999.
/
EOF
close MDIN;
system("/home/tan/amber8/exe/sander -O -i mdin -p cys_ser.prmtop -c cys_ser$out.erst -o cys_ser$out.out -r cys_ser$out.rst -x cys_ser$out.crd");
}
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- application/pdf attachment: fig.pdf
Received on Thu Jul 08 2004 - 00:53:00 PDT
