AMBER Archive (2002)

Subject: Re: ion distances

From: 남기엽 (kyn_at_camd.ssu.ac.kr)
Date: Thu Nov 21 2002 - 16:52:55 CST

> hi,
>
> how can I get the distances from the ions to the DNA,
> with either carnal or ptraj, is there a way other
> than typing explicitly all the atoms?
> thanks, Marcela

Our group published for ion distances

Chemical Physics Letters
Volume 364, Issues 5-6, 16 October 2002, Pages 580-585

Molecular dynamics simulation of Na-DMP- and Na-MP2- ion pair in aqueous solution

Nam Sook Kangb, Dong Hyun Jungb, Kyung Tai Nob and Mu Shik Jhon,

Abstract
Molecular dynamics simulations with an umbrella potential function in solution were carried out to obtain the potential of mean force for sodium-dimethyl phosphate (Na-DMP-) and sodium-methyl phosphate (Na-MP2-). The Na-DMP- showed two minima in pmf profile, a less stable minimum of ca. 3.5 Å and a more stable minimum of ca. 5.0 Å, resulting in direct and indirect contact between two ions. On the other hand, the Na-MP2- showed one prominent minimum in pmf profile, at approximately ca. 4.5 Å. Water molecules around Na-DMP- better formed a hydrogen-bonded network than around Na-MP2-, showing a stronger interaction between water and the Na-MP2-.

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Ky-Youb Nam Ph. D.
Post Doctor, CAMD Lab. of Chemistry &
CAMD Research Center, Soongsil University, Sangdo 5 dong,
Dongjak ku, Seoul, 156-743, Korea
Tel : 82-2-825-1785
Fax : 82-2-825-1795
C.P.: 011-9736-6046
email : kyn_at_camd.ssu.ac.kr
homepage : http://camd.ssu.ac.kr/~kyn
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