Dear Amber Users,
I am using pmemd.cuda single processor job run. In my equilibration step
where I want to bring my system to the required density I am using ntb=2,
ntp=2, pres0=1, taup=1.0 with time step 0.001 . After certian initial steps
my output files give NaN in TEMP and sometime the energy is very high. I
have set temp0 and tempi as 300K and temperature fluctuates a lot.
So I used a a very small time step dt=0.0002, my job runs to certain extent
and again stops . There is no error message in output file but there are
some message as below. Can you help me with where I might be making a
mistake here.
Thanks Kirtana
Nonbond cells need to be recalculated, restart simulation from previous
checkpoi
nt
with a higher value for skinnb.
sleeping
... finished
NSTEP = 10100 TIME(PS) = 1100.520 TEMP(K) = 348.27 PRESS =
-269.6
Etot = -74527.3948 EKtot = 39082.0938 EPtot =
-113609.4885
BOND = 32717.8694 ANGLE = 11701.8297 DIHED =
0.0000
1-4 NB = -3244.6814 1-4 EEL = -2704.0479 VDWAALS =
7789.3074
EELEC = -165781.7780 EHBOND = 0.0000 RESTRAINT =
5912.0123
EAMBER (non-restraint) = -119521.5008
EKCMT = 14811.4565 VIRIAL = 19110.8720 VOLUME =
738482.1312
Density =
0.9585
------------------------------------------------------------------------------
NSTEP = 10200 TIME(PS) = 1100.540 TEMP(K) = 345.40 PRESS =
-217.4
Etot = -74442.7865 EKtot = 38759.5820 EPtot =
-113202.3685
BOND = 32736.0643 ANGLE = 11538.8603 DIHED =
0.0000
1-4 NB = -3246.0456 1-4 EEL = -2710.5924 VDWAALS =
8301.0357
EELEC = -165989.5676 EHBOND = 0.0000 RESTRAINT =
6167.8768
EAMBER (non-restraint) = -119370.2453
EKCMT = 14671.2103 VIRIAL = 18137.5078 VOLUME =
738446.7256
Density =
0.9586
&cntrl
imin=0,
ntxo=1, ntrx=1,
cut=8.0, tempi=300.0, ntwprt=0,
ntpr=100, ntwx=100, ntwe=100, ntwr=100, ioutfm=0,
nstlim=100000, temp0=300.0,
dt=0.0002, nscm=100,nsnb=10,dielc=1.0,
ntc=2, ntf=2, tol=0.00001,
ntx=5, irest=1,iwrap=1,
ntb=2,ntp=2,pres0=1,taup=1.0,
ntt=3,gamma_ln=2,ig=-1,
ntr=1,restraintmask=':1-100',restraint_wt=100,
&end
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Received on Wed Jul 02 2014 - 12:00:02 PDT
