AMBER Archive (2006)

Subject: RE: AMBER: Some warning !!! during SANDER ?

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Wed Nov 22 2006 - 10:48:55 CST

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_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
jitrayut jitonnom
Sent: Wednesday, November 22, 2006 00:21
To: amber_at_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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