Dear All, I ran two control simulations on the same system (topology and
coordinates, 3437 atoms), using pmemd in the same machine conditions
(mpirun with 6 tasks/procs), with the same options in the input file,
apart from the format of the trajectory (ascii and binary, i. e.
ioutfm=0 or 1).
This is the input for both cases:
ASCII:
NVT 500K PROVA MDVEL
&cntrl
imin = 0, irest = 1, ntx = 5,
ntb = 1, pres0 = 1.0, ntp = 0,
taup = 1.0, iwrap=0,
cut = 8, ioutfm=0,
ntc = 2, ntf = 2,
temp0 = 500.0,
ntt = 1,
nstlim = 800000, dt = 0.002,
ntpr = 100, ntwx = 100, ntwr = 100, ntwv = 100
&end
BINARY:
NVT 500K PROVA MDVEL
&cntrl
imin = 0, irest = 1, ntx = 5,
ntb = 1, pres0 = 1.0, ntp = 0,
taup = 1.0, iwrap=0,
cut = 8, ioutfm=1,
ntc = 2, ntf = 2,
temp0 = 500.0,
ntt = 1,
nstlim = 800000, dt = 0.002,
ntpr = 100, ntwx = 100, ntwr = 100, ntwv = 100
&end
The final structure (restrt) is different (obviously?) owing to the
different numerical representation of the trajectory.
But what about the energy data summarized in the pmemd output file?
After some cycles, the reported energy data begin to accumulate
differences.
The final averages are these:
ASCII:
A V E R A G E S O V E R 8000 S T E P S
NSTEP = 800000 TIME(PS) = 123410.000 TEMP(K) = 500.07 PRESS =
0.0
Etot = 8094.2782 EKtot = 5121.6841 EPtot =
2972.5941
BOND = 1914.4745 ANGLE = 2356.1170 DIHED =
682.1608
1-4 NB = 167.6396 1-4 EEL = 707.7357 VDWAALS =
-2310.7221
EELEC = -544.8114 EHBOND = 0.0000 RESTRAINT =
0.0000
Ewald error estimate: 0.1476E-02
BINARY:
A V E R A G E S O V E R 8000 S T E P S
NSTEP = 800000 TIME(PS) = 123410.000 TEMP(K) = 500.07 PRESS =
0.0
Etot = 8094.2782 EKtot = 5121.6841 EPtot =
2972.5941
BOND = 1914.4745 ANGLE = 2356.1170 DIHED =
682.1608
1-4 NB = 167.6396 1-4 EEL = 707.7357 VDWAALS =
-2310.7221
EELEC = -544.8114 EHBOND = 0.0000 RESTRAINT =
0.0000
Ewald error estimate: 0.1476E-02
------------------------------------------------------------------------------
How can you explain this result? What could be the influence on the
conformations dumped in the trajectory?
Thanks a lot
Regards
Lorenzo
--
=======================================
Lorenzo Gontrani
Research associate of EDXD group
University of Rome "La Sapienza"
GSM +39 338 7615798
WORK +39 06 49693273
Email l DOT gontrani AT caspur DOT it
Webpage: http://webcaminiti/gontrani.html
=======================================
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Received on Wed Jun 01 2011 - 03:00:02 PDT
