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From: Xiaowei (David) Li <"Xiaowei>

Date: Sun, 05 Dec 2004 12:42:56 -0500

Dear AMBER users:

It is widely used technique to mimic the the influence of solvent using

implicit solvent(Generally, water). In AMBER, my understanding is that

there are two methods to use implicit solvent. One is Generalized-Born

(GB) model , and the other is to use distance-dependent dielectric

model. Beause there is no GB model implemented in NMODE, so I use

distantce-dependent dielectic model when I perform normal mode analysis

of nucleic acids. My question is concering about the distance-dependent

model in AMBER.

Based on the Debye-Hückel model, the screened Coulomb potential (phi) is

phi=(Z*q)/(epsilon *r) exp(-kr), here the 1/k is the D-H length, epsilon

is the dielectric constant in vacumm.

Therefore, the effective dielectric constant is (epsilon * exp(kr)). If

|kr|<1, then exp(kr) is approximated as (1+kr). So the effective

dielectric constant is (epsilon*(1+kr)).

In NMODE, we can set dielc=1-4 and idiel=0 to get the effective

dielectric constant as (1-4)*r, which means kr>>1 and the dielectric

constant is distant dependent. However, if the amount of water is very

small, then k is very close to 0. Thus, we should set the dielectric

constant as (epsilon*(1+kr)), instead of (epsilon*kr). But it seems to

me that there is no options in AMBER to set the dielectric constant as

(epsilon*(1+kr)). In other words, we can set constant dielectric or

distant-dependent dielectric constant in AMBER. But there is

discontinuity between these two cases. This is my understanding about

this question. If I am wrong, please feel free to correct me. Thank you

very much.

Best,

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Received on Sun Dec 05 2004 - 17:53:00 PST

Date: Sun, 05 Dec 2004 12:42:56 -0500

Dear AMBER users:

It is widely used technique to mimic the the influence of solvent using

implicit solvent(Generally, water). In AMBER, my understanding is that

there are two methods to use implicit solvent. One is Generalized-Born

(GB) model , and the other is to use distance-dependent dielectric

model. Beause there is no GB model implemented in NMODE, so I use

distantce-dependent dielectic model when I perform normal mode analysis

of nucleic acids. My question is concering about the distance-dependent

model in AMBER.

Based on the Debye-Hückel model, the screened Coulomb potential (phi) is

phi=(Z*q)/(epsilon *r) exp(-kr), here the 1/k is the D-H length, epsilon

is the dielectric constant in vacumm.

Therefore, the effective dielectric constant is (epsilon * exp(kr)). If

|kr|<1, then exp(kr) is approximated as (1+kr). So the effective

dielectric constant is (epsilon*(1+kr)).

In NMODE, we can set dielc=1-4 and idiel=0 to get the effective

dielectric constant as (1-4)*r, which means kr>>1 and the dielectric

constant is distant dependent. However, if the amount of water is very

small, then k is very close to 0. Thus, we should set the dielectric

constant as (epsilon*(1+kr)), instead of (epsilon*kr). But it seems to

me that there is no options in AMBER to set the dielectric constant as

(epsilon*(1+kr)). In other words, we can set constant dielectric or

distant-dependent dielectric constant in AMBER. But there is

discontinuity between these two cases. This is my understanding about

this question. If I am wrong, please feel free to correct me. Thank you

very much.

Best,

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

The AMBER Mail Reflector

To post, send mail to amber.scripps.edu

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

Received on Sun Dec 05 2004 - 17:53:00 PST

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