AMBER Archive (2002)

Subject: difference in energy in amber6 and amber7

From: Prabal Maiti (maiti_at_wag.caltech.edu)
Date: Mon Dec 09 2002 - 20:07:15 CST

Dear Amber Users,
When I use amber7 on to continue my dynamics runs I get different energy
compared to amber6 runs. Can someone suggest which parameters (default
etc) needs to be specified to get exactly same energy. The inital energy
is same in both amber6 and amber7. But during the dynamics energy differs.

This is with AMBER6

------------------------------------------------------------------------------
 NSTEP = 0 TIME(PS) = 277.000 TEMP(K) = 300.63 PRESS = 0.00
 Etot = -159862.8382 EKtot = 28694.0102 EPtot = -188556.8484
 BOND = 1455.5963 ANGLE = 3250.5259 DIHED = 3429.8863
 1-4 NB = 1514.0884 1-4 EEL = -20658.9143 VDWAALS = 15968.8940
 EELEC = -193516.9249 EHBOND = 0.0000 CONSTRAINT = 0.0000
 Ewald error estimate: 0.9672E-05
 
------------------------------------------------------------------------------

 NSTEP = 100 TIME(PS) = 277.200 TEMP(K) = 301.05 PRESS = 0.00
 Etot = -159580.4931 EKtot = 28733.8403 EPtot = -188314.3334
 BOND = 1520.1264 ANGLE = 3261.2512 DIHED = 3454.1387
 1-4 NB = 1538.3140 1-4 EEL = -20677.8454 VDWAALS = 15789.6256
 EELEC = -193199.9439 EHBOND = 0.0000 CONSTRAINT = 0.0000
 Ewald error estimate: 0.6369E-04
 
------------------------------------------------------------------------------

This is with AMBER7

------------------------------------------------------------------------------
NSTEP = 0 TIME(PS) = 277.000 TEMP(K) = 300.63 PRESS = 0.0
 Etot = -159862.8382 EKtot = 28694.0102 EPtot = -188556.8484
 BOND = 1455.5963 ANGLE = 3250.5259 DIHED = 3429.8863
 1-4 NB = 1514.0884 1-4 EEL = -20658.9143 VDWAALS = 15968.8940
 EELEC = -193516.9249 EHBOND = 0.0000 RESTRAINT = 0.0000
 Ewald error estimate: 0.9672E-05
 
------------------------------------------------------------------------------

 NSTEP = 100 TIME(PS) = 277.200 TEMP(K) = 298.08 PRESS = 0.0
 Etot = -159834.5074 EKtot = 28450.6167 EPtot = -188285.1241
 BOND = 1521.3677 ANGLE = 3263.3566 DIHED = 3454.7686
 1-4 NB = 1538.4880 1-4 EEL = -20677.9441 VDWAALS = 15789.6414
 EELEC = -193174.8023 EHBOND = 0.0000 RESTRAINT = 0.0000
 Ewald error estimate: 0.6277E-04
 
----------------------------------------------------------------------------
Also how accurate is PME. In amebr6 run I had nfft1=45 and in amber7
nfft1=48 (it does not accept odd number) and the electrostatics energy is
different by 100 kcal/mol though the change is less than 1%. So the grid
spacing is not fine enough.

Prabal 

-- 
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Prabal K Maiti                             Email:maiti_at_wag.caltech.edu
Beckman Institute (139-74)                       pkmaiti_at_yahoo.com
California Institute of Technology         Tel:626-395-8151 (O)
400 South Wilson Avenue                       :626-744-1363 (H)                    
Pasadena, CA 91125                         Fax:626-585-0918
                                           Home add: 110 S. Michigan Ave.
http://www.wag.caltech.edu/home/maiti      Apt # 19, Pasadena, CA 91106
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