Hello,
I am trying to use the DEBUG option in Generalised Born MD simulation
and getting nonsensical energies and forces. I have tried this
for several different systems, including the two GB tutorials, with
similar errors. I have tried this on two different machines, a Silicon
Graphics R10000 and a Linux cluster, with similar errors. The MD runs
fine for all systems when the DEBUG section is removed.
My input file is below, along with a few lines of the output. Could
anyone please offer me any ideas on what is going on?
Thank you in advance.
Garth
md.in
=================================================
&cntrl
ntc=2, ntf=2,
cut=12.0, igb=2, saltcon=0.2, gbsa=0,
ntpr=50, ntwx=50,
nstlim = 500, dt=0.002,
ntt=1, tempi=300.0, temp0=300.0, tautp=2.0,
ntx=1, irest=0, ntb=0,
nscm = 1000,
&end
&debugf
neglgdel=4, nranatm=25, atomn=0,
do_debugf=1, do_dir=0, do_adj=0, do_rec=1, do_self=0,
do_bond=1, do_angle=0, do_ephi=0, zerovdw=0, zerochg=0,
chkvir=0,
dumpfrc=1,
rmsfrc=0,
&end
md.out
..
..
..
DEBUG FORCE!; calling force routine
DEBUG FORCE!; back from force routine
NSTEP = 0 TIME(PS) = 10.000 TEMP(K) = 0.00 PRESS =
0.0
Etot = ************ EKtot = 0.0000 EPtot =
************
BOND = 274.2593 ANGLE = 0.0000 DIHED =
0.0000
1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS =
-792.5538
EELEC = ************ EGB = ************ RESTRAINT =
0.0000
ESURF = 27.8601
..
..
..
..
NUMERICAL, ANALYTICAL FORCES from atom 1480
1 0.00000000 0.00000000
2 0.00000000 0.00000000
3 0.00000000 0.00000000
RMS force error = 0.000E+00
NUMERICAL, ANALYTICAL FORCES from atom 988
..
..
..
NUMERICAL, ANALYTICAL FORCES from atom 7
1************** **************
2************** **************
3************** **************
RMS force error = 0.937E+00
NUMERICAL, ANALYTICAL FORCES from atom 1362
..
..
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Received on Tue May 18 2004 - 13:53:00 PDT
