Hi Amber users,
I'm comparing the energy output of Sander and anal. To do so I have
performed with sander a "single point" energy calculation in vacuo on a
very simple system and use the restart point as the input for anal.
GLY: H---N O
\ /
CH2---C
\
O
Unfortunately I wasn't able to obtain the same energies. Especially I
don't understand the difference observed for the non-bonded parameters.
I have also performed a test with the MMC software. The calculated
non-bonded energies are in very good agreement with those obtain with
anal but differ from the sander's ones .
here is a summery of the observed energies
------------------------------------------------------------------
Sander | Anal | MMC |
------------------------------------------------------------------
Etot -.8079680237E+02 | 13.6904 | |
E_pot -.8122887215E+02 | | |
E_vdw -.6843000450E-02 | -0.0075 | -0.0075|
E_el -.3385359257E+02 | -34.3752 | -34.3775|
E_hbon -.9543817545E+02 | 0.0000 | |
E_bon 0.7204055278E+00 | 0.6606 | |
E_angle 0.2806542542E+01 | 2.7132 | |
E_dih 0.1283584851E-01 | 0.0123 | |
E_14vdw 0.9771176270E+00 | 0.9415 | 0.9420|
E_14el 0.4355283732E+02 | 43.7454 | 43.7530|
------------------------------------------------------------------
Is anybody can explain why the energy term obtain from Sander are
different ?
Thank you in advance.
-----------------------------------------------------------------------------
Here is my input file for Sander
&cntrlHere is my input file for Sander
imin=0, ntx=1, ntpr=1, ntwr=1, ntwx=1, ntwe=1,
nscm=5000,
ntf=2, ntc=2,
ntb=0, igb=2
nstlim=1, t=0.0, dt=0.002,
cut=999.0,
irest=0
&end
-----------------------------------------------------------------------------
Here is my input file for Anal
ANAL ENERGY EXTRACTION
1 0 0 0 0 1
0 0.0000 0.0000 0.0000 0.0
1 0 0 1 50 1
999.0 2 1.2 1
0
ENERGY
Energy Analysis
RES 1
END
END
STOP
-----------------------------------------------------------------------------
--
--------------------------------------------------------------------------------
Emmanuel GIUDICE
--------------------------------------------------------------------------------
MOUNT SINAI SCHOOL OF MEDICINE
DEPARTMENT OF PHYSIOLOGY AND BIOPHYSICS Emmanuel.Giudice.mssm.edu
One Gustave L. Levy place, Annenberg Building Tel-Labo : (212) 241-1613
21st Floor, Room 78 New York, NY 10029 Fax : (212) 860-3369
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Received on Wed Jan 14 2004 - 15:53:03 PST
