Re: different values of "1-4scaling" in a system

From: Chris Harrison (char_at_ks.uiuc.edu)
Date: Fri Jun 18 2010 - 11:49:49 CDT

Daisuke,

"1-4 nonbonded interactions, involving atoms separated by three covalent
bonds, do have nonbonded contributions as well as their spatial relationship
being influenced by the internal terms, including the dihedral term.
However different biomolecular force fields treat the 1-4 nonbonded
interactions differently"

Now that that's out of the way, NAMD only supports a 1-4 scaling term that's
consistent across all 1-4 terms in the selected forcefield (ff), as do (as
far as I know) all other MD programs. It is rather 'odd' to have differing
1-4 scaling within the same ff, though of course 1-4 *terms* are common.

I would suggest that the most efficient route to properly resolving your 1-4
term differences would be to re-parameterize the 1-4 terms in your modified
ff.

Best,
Chris

On Wed, Jun 16, 2010 at 6:00 AM, D70039 <takaiwa-dai_at_aist.go.jp> wrote:

> Hi all,
>
> I’m trying to run NAMD with mixture of the original CHARMM force field and
> a modified CHARMM force filed. One of the differences between the original
> version and the modified version is value of the keyword "1-4scaling" in
> configure file.
>
> By the way, "1-4scaling" is used to change the electrostatic interactions
> between 1-4 atom pairs to my knowledge.
>
> If the scale factors are different for different atom types as this , what
> should I do for the configure file ?
> Thanks in adavnce,
>
> Daisuke Takaiwa
>
> ========================================
>
> Daisuke Takaiwa
>
> Nanosystem Research Institute(NRI)
> National Institute of Advanced Industrial Science and Technology(AIST)
> 1-1-1 Umezono, Tsukuba 305-8568, JAPAN
>
> E-mail takaiwa-dai_at_aist.go.jp
>
> 

-- 
Chris Harrison, Ph.D.
Theoretical and Computational Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
char_at_ks.uiuc.edu                            Voice: 217-244-1733
http://www.ks.uiuc.edu/~char               Fax: 217-244-6078

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