Hello,
I have been running pmemd.cuda on several different
small peptide systems. After minimization and equilibration
with sander I run md with pmemd.cuda which produces the
following output in the mdinfo file:
NSTEP = 1000 TIME(PS) = 419.000 TEMP(K) = 312.76 PRESS =
0.0
Etot = ************** EKtot = 300.8112 EPtot =
**************
BOND = 80.7068 ANGLE = 182.6906 DIHED =
292.4277
1-4 NB = 85.6465 1-4 EEL = 1165.3455 VDWAALS =
**************
EELEC = ************** EGB = -448.5671 RESTRAINT =
0.0000
Howerver, running with sander.MPI or pmemd.MPI both produce the following
output in the mdinfo file:
NSTEP = 185000 TIME(PS) = 405.000 TEMP(K) = 286.55 PRESS =
0.0
Etot = -216.4261 EKtot = 275.6074 EPtot =
-492.0335
BOND = 80.9310 ANGLE = 212.0786 DIHED =
294.2501
1-4 NB = 86.1050 1-4 EEL = 1157.8286 VDWAALS =
-114.6716
EELEC = -1741.2225 EGB = -467.3327 RESTRAINT =
0.0000
Here is the input file I used for running the tests:
CYC MD
&cntrl
imin=0,irest=1,ntx=5,
nstlim=25000000,dt=0.002,ntb=0,
tempi=300, temp0=300,
ntf=2,ntc=2,tol=0.000001,
ntpr=1000, ntwx=1000, ntwr=1000,
cut=9999.0, rgbmax=15.0,gbsa=0,
igb=5,ntt=3,nscm=1000,gamma_ln = 1.0
/
This was pretty painful to workout so I think it might be a bug in
pmemd.cuda. I
should also say I tried running it on two different cards with the same
outcome.
Thanks!
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Received on Sat Apr 24 2010 - 16:30:03 PDT
