Dear Jitrayut,
Check Com Veclocity is just an informational message concerning the removal
of center of mass motion. This is controlled by the namelist variable nscm.
The default is every 1000 steps. You can safely ignore these messages.
All the best
Ross
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From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of
jitrayut jitonnom
Sent: Wednesday, November 22, 2006 00:21
To: amber.scripps.edu
Subject: AMBER: Some warning !!! during SANDER ?
Dear amber users,
I was wondering that what is this errors that shown below. Should i concern
about this ? Indeed, i do md from different program, what i do is i run md
in amber9 and then send it run md again in amber 8 and i found these errors
that what i have done. So, any suggestions for this problems will be
appreciated.
Thanks in advanced,
Jitrayut
The errors are here,
check COM velocity, temp: 0.002738 0.01(Removed)
check COM velocity, temp: 0.003472 0.02(Removed)
check COM velocity, temp: 0.002469 0.01(Removed)
check COM velocity, temp: 0.003645 0.02(Removed)
check COM velocity, temp: 0.001310 0.00(Removed)
NSTEP = 190000 TIME(PS) = 980.000 TEMP(K) = 298.00 PRESS =
-187.0
Etot = -82550.4880 EKtot = 20391.7127 EPtot =
-102942.2008
BOND = 676.2643 ANGLE = 1842.5703 DIHED =
2268.6225
1-4 NB = 776.3001 1-4 EEL = 7245.6266 VDWAALS =
11906.0515
EELEC = -127657.6361 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 8923.4190 VIRIAL = 10276.1024 VOLUME =
335112.6119
Density =
1.0192
Ewald error estimate: 0.1119E-03
----------------------------------------------------------------------------
--
check COM velocity, temp: 0.003755 0.02(Removed)
check COM velocity, temp: 0.005429 0.04(Removed)
check COM velocity, temp: 0.001142 0.00(Removed)
check COM velocity, temp: 0.002623 0.01(Removed)
check COM velocity, temp: 0.003282 0.02(Removed)
NSTEP = 195000 TIME(PS) = 990.000 TEMP(K) = 299.55 PRESS =
-85.7
Etot = -82620.1216 EKtot = 20497.7907 EPtot =
-103117.9124
BOND = 698.4432 ANGLE = 1775.4316 DIHED =
2296.6966
1-4 NB = 781.5175 1-4 EEL = 7272.9965 VDWAALS =
12071.5318
EELEC = -128014.5295 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 9072.2442 VIRIAL = 9693.0794 VOLUME =
335372.8362
Density =
1.0185
Ewald error estimate: 0.5392E-04
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Received on Wed Nov 22 2006 - 23:01:51 PST
