AMBER Archive (2005)

Subject: AMBER: MMGBSA and dielectric constant with AMBER8 - dielc and intdiel

From: Fabien Cailliez (Fabien.Cailliez_at_ibpc.fr)
Date: Tue Feb 08 2005 - 11:16:51 CST

Dear all,

I have a question about dielectric constant in MMGBSA calculation with
AMBER8.
When I tried to put intdiel=2, I had a message that said me thta intdiel
must be equal to dielc.
Thus I put dielc=2 too, but I am confused with the results I obtained.
Here is an example of one calculation with a dielectric constant of 1
and 2 :
***** dielc and intdiel=1
1
 BOND = 674.6114 ANGLE = 1662.9186 DIHED =
2067.4398
 VDWAALS = -1487.8876 EEL = -15883.4589 EGB =
-3734.9502
 1-4 VDW = 754.7371 1-4 EEL = 9784.9053 RESTRAINT =
0.0000
surface area = 12257.6574
***** dielc and intdiel=2
1
 BOND = 674.6114 ANGLE = 1662.9186 DIHED =
2067.4398
 VDWAALS = -1487.8876 EEL = -3970.8647 EGB =
-924.1456
 1-4 VDW = 754.7371 1-4 EEL = 2446.2263 RESTRAINT =
0.0000
surface area = 12257.6574

As you can see, when I put dielc and intdiel=2, I have all the
electrostatic contributions (EEL, 1-4 EEL, and GB) divided by
approximately 4.
I thought that the results shoud be divided by approximately 2 (and not
4). I guess that dielc should not be set to 2 if
intdiel=2.
Am I right or wrong ? Should the energies be divided by 2 or 4 when
dielectric constant is multiplied by 2 ?

Thanks for your help,
Fabien

PS : I went through the code and I understood that when dielc is set to
2, the charges are divided by sqrt(2), so this is one
division by 2. For GB, there is another division by intdiel in egb.f, so
that makes the whole thing divided by 4. This is the same
for 1-4EEL in subroutine ephi. But I could not find where EEL is
calculated (somewhere in ewald_force I guess) 

-- 
__________________________________________________________________
Fabien Cailliez				Tel : 01 58 41 51 63				
Laboratoire de Biochimie Théorique	e-mail : cailliez_at_ibpc.fr
IBPC	13, rue Pierre et Marie Curie 		
75005 Paris					
__________________________________________________________________

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu