Someone here is trying to do a charge perturbation in Amber9.
He is successful when he uses a cap with igb=10, but not
otherwise (with other variables controlled: same two top
files, etc.).
It doesn't look like an input issue because when it isn't
successful, the job goes for a few thousand steps and seems to
just hang (using cpu according to top, but not writing any
output for, like, 20 hours). If it were an input issue, it
probably wouldn't go at all. Feel free to disagree, of course.
He says he was able to not use igb=10 in Amber8.
Here are the input files:
This one works in Amber8 but not Amber9:
water coulomb
&cntrl
ntr=0, ivcap=0, fcap=10.0,
nstlim=100000,
ntx=5, irest=1, ntpr=1000, tempi=300.0, temp0=300.0,
dt=0.001, ntt=1, ntb=0, tautp=0.1,
ntc=2, ntf=2, tol=0.000001,
ntwr=10000, ntwx=0,cut=10.0,
icfe=1, klambda=1, clambda=0.11270,
/
This one works (gives output, finishes) in both Amber8 and Amber9:
water coulomb
&cntrl
ntr=0, igb=10, ivcap=0, fcap=10.0,
nstlim=100000,
ntx=5, irest=1, ntpr=1000, tempi=300.0, temp0=300.0,
dt=0.001, ntt=1, ntb=0, tautp=0.1,
ntc=2, ntf=2, tol=0.000001,
ntwr=10000, ntwx=0,
icfe=1, klambda=1, clambda=0.11270,
/
&pb
npbverb=1, npbgrid=100,
nsnbr=20, nsnba=4, cutres=15, cutnb=9, cutfd=9,
epsin=1.0, epsout=80.0, smoothopt=1, space=0.7, dbfopt=0
/
Help?
Thanks!
:-) Lachele
B. Lachele Foley, PhD, '02
Assistant Research Scientist
Complex Carbohydrate Research Center, UGA
706-542-0263
lfoley.uga.edu
Received on Wed Apr 05 2006 - 23:49:41 PDT
