AMBER Archive (2003)

Subject: AMBER: comparing versions 6.0 and 7.0 of AMBER

From: Therese Malliavin (Therese.Malliavin_at_ibpc.fr)
Date: Mon Oct 27 2003 - 03:30:21 CST

Dear AMBER-Netters,

I am now testing the version 7.0 of AMBER and comparing it to version
6.0

1) I was really happy that, on a cluster of Power4 IBM, the CPU time was
30% shorter for 7.0 than for 6.0 in a MD simulation.

2) I realized that the ndfmin and ntcm input parameters are no more
existing in AMBER 7.0, which is to my sense an improvement. Are there
other modifications of the input between the 2 versions, and where are
they listed (I looked in the Web site, but did not find anything) ?

3) I compared the results obtained with AMBER 6.0 and 7.0 starting with
the same input. The mean values of energies, temperature and pressure,
on 300 ps of MD simulation are of the same order, but slightly different
(see below). The differences are already visible after the first 250
steps of the simulation. Did you try similar comparisons ?

Thank you for your answers,

Thérèse Malliavin
Laboratoire de Biochimie Théorique
IBPC, Paris
France

AMBER 7.0
 NSTEP = 250 TIME(PS) = 35.500 TEMP(K) = 296.68 PRESS =
44.2
 Etot = -51368.9961 EKtot = 11952.8837 EPtot =
-63321.8797
 BOND = 250.1802 ANGLE = 803.0923 DIHED =
535.9939
 1-4 NB = 330.3660 1-4 EEL = 1450.1109 VDWAALS =
8012.4293
 EELEC = -74704.0523 EHBOND = 0.0000 RESTRAINT =
0.0000
 EKCMT = 5591.7403 VIRIAL = 5401.0442 VOLUME =
200033.5357
                                                Density =
1.0057
 Ewald error estimate: 0.1345E-03

------------------------------------------------------------------------------
 
      A V E R A G E S O V E R 150000 S T E P S
 
 
 NSTEP = 150000 TIME(PS) = 335.000 TEMP(K) = 297.84 PRESS =
1.1
 Etot = -51675.2585 EKtot = 11999.7269 EPtot =
-63674.9854
 BOND = 286.8138 ANGLE = 828.2833 DIHED =
492.1864
 1-4 NB = 319.9926 1-4 EEL = 1560.9264 VDWAALS =
7965.0759
 EELEC = -75128.2637 EHBOND = 0.0000 RESTRAINT =
0.0000
 EKCMT = 5487.5470 VIRIAL = 5482.8556 VOLUME =
199336.7664
                                                Density =
1.0093
 Ewald error estimate: 0.8209E-04

------------------------------------------------------------------------------
 
 
      R M S F L U C T U A T I O N S
 
 
 NSTEP = 150000 TIME(PS) = 335.000 TEMP(K) = 1.64 PRESS =
108.4
 Etot = 58.0769 EKtot = 65.8940 EPtot =
87.0540
 BOND = 14.2855 ANGLE = 20.7062 DIHED =
13.3836
 1-4 NB = 7.7735 1-4 EEL = 40.9783 VDWAALS =
87.1298
 EELEC = 135.5214 EHBOND = 0.0000 RESTRAINT =
0.0000
 EKCMT = 51.5177 VIRIAL = 472.8587 VOLUME =
504.3893
                                                Density =
0.0026
 Ewald error estimate: 0.6058E-04

------------------------------------------------------------------------------

AMBER 6.0
 
 NSTEP = 250 TIME(PS) = 35.500 TEMP(K) = 299.69 PRESS =
32.84
 Etot = -51294.4939 EKtot = 12075.1683 EPtot =
-63369.6622
 BOND = 253.2897 ANGLE = 805.5442 DIHED =
537.8691
 1-4 NB = 330.0391 1-4 EEL = 1452.1585 VDWAALS =
7948.0344
 EELEC = -74696.5973 EHBOND = 0.0000 CONSTRAINT =
0.0000
 EKCMT = 5557.3655 VIRIAL = 5415.6249 VOLUME =
199878.1326
                                                Density =
1.0065
 Ewald error estimate: 0.1301E-04

------------------------------------------------------------------------------
 
      A V E R A G E S O V E R ***** S T E P S
 
 
 NSTEP =150000 TIME(PS) = 335.000 TEMP(K) = 298.00 PRESS =
0.99
 Etot = -51900.6808 EKtot = 12006.9748 EPtot =
-63907.6556
 BOND = 286.7658 ANGLE = 827.3234 DIHED =
483.6268
 1-4 NB = 320.9856 1-4 EEL = 1548.5629 VDWAALS =
8024.9745
 EELEC = -75399.8945 EHBOND = 0.0000 CONSTRAINT =
0.0000
 EKCMT = 5438.0421 VIRIAL = 5433.7916 VOLUME =
198855.8801
                                                Density =
1.0117
 Ewald error estimate: 0.7820E-04

------------------------------------------------------------------------------
 
 
      R M S F L U C T U A T I O N S
 
 
 NSTEP =150000 TIME(PS) = 335.000 TEMP(K) = 1.61 PRESS =
118.65
 Etot = 86.3695 EKtot = 65.0466 EPtot =
102.2181
 BOND = 14.3055 ANGLE = 20.6284 DIHED =
15.7263
 1-4 NB = 7.9256 1-4 EEL = 35.5736 VDWAALS =
86.0490
 EELEC = 149.9105 EHBOND = 0.0000 CONSTRAINT =
0.0000
 EKCMT = 50.7803 VIRIAL = 515.9662 VOLUME =
548.7427
                                                Density =
0.0028
 Ewald error estimate: 0.5846E-04

------------------------------------------------------------------------------

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu