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From: Fabien Cailliez <Fabien.Cailliez.ibpc.fr>

Date: Tue, 08 Feb 2005 18:16:51 +0100

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)

Date: Tue, 08 Feb 2005 18:16:51 +0100

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.ibpc.fr IBPC 13, rue Pierre et Marie Curie 75005 Paris __________________________________________________________________ ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to amber.scripps.edu To unsubscribe, send "unsubscribe amber" to majordomo.scripps.eduReceived on Tue Feb 08 2005 - 17:53:00 PST

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