AMBER Archive (2006)

Subject: AMBER: EGB term decomposition

From: backy (backy_at_ibms.sinica.edu.tw)
Date: Sat Sep 09 2006 - 03:57:43 CDT

Dear Amber users:

I try to use the mm_pbsa.pl to decompose the different energy terms of a single molecule.

Actually, it seems that every thing is ok, except the EGB term.

Here is the produced mdinfo file.

 NSTEP ENERGY RMS GMAX NAME NUMBER
      1 1.6197E+03 2.0651E+02 8.2721E+03 HB3 2349

 BOND = 302.7587 ANGLE = 2640.9345 DIHED = 2907.3869
 VDWAALS = -1129.9499 EEL = -20890.3479 EGB = -4268.5653
 1-4 VDW = 6635.6331 1-4 EEL = 15355.7369 RESTRAINT = 0.0000
 ESURF = 66.1334
 

For double checking if any made mistakes, so I try to get the summation of each column from the attached file and compared it with the corresponding value in the mdinfo.

For most energy terms, int, vdw, eel and gas, the summations are almost identical to the value provided by mdinfo file, except the EGB term. In the following list, the first appearing number is the summation and the second one is from the mdinfo.

Therefore, you could see the bigger difference in EGB term.

INT 5851.07 5851.0801
VDW 5505.84 5505.6832
EEL -5534.65 -5534.611
GAS 5822.1 5822.1523
EGB -4263.96 -4268.5653 -------->bigger difference, note: -4263.96 are got by the the summation of those values in TGB column of the attached file.

Is there anything wrong?

Thanks for helping.

backy

         
 


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