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From: Cenk Andac <cenk_andac.yahoo.com>

Date: Wed, 4 May 2005 13:52:06 -0700 (PDT)

Dear amber members,

I have done some dipole moment computations for a

covalently connected C-N atom

pair in a molecule.

I understand that the vectorial direction of

permanent

dipole moment for the atom pairs should be from N to C

(N ---> C) since N has more negative

partial charge than C. In that case, I guess N is the

center of mass for the atom pairs.

My question is about the induced dipole moment

computations for the atom pairs.

How would AMBER8 treat the atom pairs to compute an

induced dipole moment?

Is it something that AMBER8 computes induced dipole

moments for each atom separately

based on their polarizibility and the electric field

applied on each of the atoms, then the

induced dipole moments are summed up to yield a total

induced dipole moment for the atom pairs?

Or is it something that AMBER8 sees the atom pairs as

a whole ? Then what would be the polarizibility for

the whole system?

Another question, does AMBER8 needs to find a center

of mass to compute induced dipole moment

for a pair of atoms? (my answer would be "NO", but I

just want to make sure here)

Thanks,

jenk.

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Received on Wed May 04 2005 - 22:53:00 PDT

Date: Wed, 4 May 2005 13:52:06 -0700 (PDT)

Dear amber members,

I have done some dipole moment computations for a

covalently connected C-N atom

pair in a molecule.

I understand that the vectorial direction of

permanent

dipole moment for the atom pairs should be from N to C

(N ---> C) since N has more negative

partial charge than C. In that case, I guess N is the

center of mass for the atom pairs.

My question is about the induced dipole moment

computations for the atom pairs.

How would AMBER8 treat the atom pairs to compute an

induced dipole moment?

Is it something that AMBER8 computes induced dipole

moments for each atom separately

based on their polarizibility and the electric field

applied on each of the atoms, then the

induced dipole moments are summed up to yield a total

induced dipole moment for the atom pairs?

Or is it something that AMBER8 sees the atom pairs as

a whole ? Then what would be the polarizibility for

the whole system?

Another question, does AMBER8 needs to find a center

of mass to compute induced dipole moment

for a pair of atoms? (my answer would be "NO", but I

just want to make sure here)

Thanks,

jenk.

__________________________________

Do you Yahoo!?

Make Yahoo! your home page

http://www.yahoo.com/r/hs

-----------------------------------------------------------------------

The AMBER Mail Reflector

To post, send mail to amber.scripps.edu

To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu

Received on Wed May 04 2005 - 22:53:00 PDT

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