From: AnkiReddy katha (kathaankireddy_at_gmail.com)
Date: Thu May 07 2015 - 04:40:47 CDT
Dear NAMD users
I found a post related to the question i asked .
http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2011-2012/1263.html
Thank you
Best Regards
Anki
On Thu, May 7, 2015 at 2:47 PM, AnkiReddy katha <kathaankireddy_at_gmail.com>
wrote:
> Dear NAMD users
>
> I am trying to use OPLS force field in NAMD.
>
> vdwGeometricSigma yes
> 1-4 scaling 0.5
>
> The above are changes we need to make for non-bonded interactions.
>
> Bonded interactions (bonds term and angle term) needs no change as both
> OPLS and CHARMM type used same expressions.
>
> Dihedral term expression also is similar, so one can easily adapt OPLS
> dihedral parameters into the CHARMM type.
>
> There seems to be an issue with Improper style.
>
> OPLS force field uses periodic improper dihedral, CHARMM type uses
> harmonic improper dihedral
>
> One idea I had was that we can have have impropers and propers under the single
> head "dihedrals" in the parameter file, like OPLS style as shown below.
>
> 74 21 5 9 8 OPLS_IMPROPER 0.000000 0.000000 2.000000 0.000000 0.000000 0.000000 0.000000
> 75 15 11 10 5 OPLS_IMPROPER 0.000000 0.000000 8.000000 0.000000 0.000000 0.000000 0.000000
>
> If we do that, then NAMD may not calculate "improper" energy term explicitly, however it includes in the "dihedral".
>
> Also it may consider 1-4 interactions between the atoms which are 1 and 4 atoms, which are actually not separated by three
>
> bonds.
>
> If some of you have used OPLS in NAMD, could you please clarify how you handled OPLS_impropers.
>
> Thank you very much
>
> Best Regards
>
> Anki
>
>
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