Dear all,
I finished my simulation which is the organic molecule
in the water box. By now I would like to calculate the
binding energy of solute and solvent. I extracted the
coordinate from the trajectory and then calculated the
energy by using sander. I used this equation :
Ebinding = E(mol + Wat ) - E (mol) -E(Wat)
The E (mol) is calculated in gas phase. Form the
results I got very difference 1-4 Electrostatic
energy.
--------------------------------------------------
mol+Wat mol Wat
1-4 EEl -40 -230 0
EEl -11747 70 -11707
1-4VDW 12 12 0
--------------------------------------------------
I don't understand the why I got difference value in
1-4 EEl. Can I evaluate the interation as I told you?
Thank you in advance.
TK
__________________________________
Do you Yahoo!?
Read only the mail you want - Yahoo! Mail SpamGuard.
http://promotions.yahoo.com/new_mail
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Tue Dec 07 2004 - 17:53:00 PST
