AMBER Archive (2003)

Subject: AMBER: Sander / Anal

From: Emmanuel Giudice (Emmanuel.Giudice_at_mssm.edu)
Date: Mon Dec 01 2003 - 14:06:00 CST

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_at_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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