Sorry if this is a repeat, my emails don't seem to be going through.
Hi,
I have been running MD simulations on a gpu and am having issues when
restarting. I have ntt=2 and when restarting on gpu the first step has a
temperature of about 2000 instead of 300. I have irest=1 and ntx=5 so
velocity information should be read from the restart file. The restart
files are there and have information in them. When I run the same
simulations on cpu using the exact same input files the temperature does
not spike like this. Has anyone seen this before or know what might be
causing it? I am using Amber11 but I have also tried Amber12 and I still
have the same issue.
Thanks for your help,
Sarah Graham
input file
Production run
&cntrl
imin = 0,
irest = 1, ntx = 5,
ntwe = 1000, ntwx = 1000, ntwr = 1000, ntpr = 1000, ntwv = 1000,
ntt = 2, temp0 = 300.0, tempi = 300.0,
dielc = 1, cut = 10.0,
ntb = 2, ntp = 1, ntc = 2, ntf = 2,
ig = -1,
nstlim = 1250000, dt = 0.0020,
/
example output
|-----------------------------
----------------------
Setting new random velocities at step 1000
check COM velocity, temp: 0.004194 0.03(Removed)
NSTEP = 1000 TIME(PS) = 69332.000 TEMP(K) = 1860.02 PRESS =
-154.1
Etot = 28134.4824 EKtot = 174025.4076 EPtot =
-145890.9252
BOND = 696.4149 ANGLE = 1824.4578 DIHED =
2475.8020
1-4 NB = 833.1366 1-4 EEL = 8244.7069 VDWAALS =
17977.2913
EELEC = -177942.7347 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 12792.8104 VIRIAL = 14330.6250 VOLUME =
462044.0055
Density =
1.0133
------------------------------------------------------------------------------
Setting new random velocities at step 2000
check COM velocity, temp: 0.000951 0.00(Removed)
NSTEP = 2000 TIME(PS) = 69334.000 TEMP(K) = 300.63 PRESS =
-54.6
Etot = -117857.7631 EKtot = 28126.8179 EPtot =
-145984.5810
BOND = 734.8103 ANGLE = 1823.5534 DIHED =
2467.0220
1-4 NB = 852.7348 1-4 EEL = 8202.9194 VDWAALS =
17875.8311
EELEC = -177941.4521 EHBOND = 0.0000 RESTRAINT =
0.0000
203,2 1%
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Received on Mon Jun 10 2013 - 05:30:03 PDT
