VMD-L Mailing List

From: Mayne, Christopher G (cmayne2_at_illinois.edu)
Date: Thu Sep 13 2012 - 19:58:48 CDT

As far as I know, most MD engines will use multiple periodicities (i.e. n=1 & n=3 from your data) additively in the energy evaluation; which is why we put that option in ffTK. If you look through the standard CHARMM distribution, it is a fairly common way of fitting complex dihedral profiles, but is not without its drawbacks and limitations. For a good discussion, see:

http://mackerell.umaryland.edu/~kenno/cgenff/faq.html#multi

Chris

On Sep 13, 2012, at 6:53 PM, ehsan zahedinejad wrote:

> Dear VMD users,
>
> After successfully generating ff parameters using VMD fftk I have a question about duplicate option in fftk. I used this option to get the best dihedral fit. After extracting ff from dihedral I noticed there are two set of dihedrals for one of my dihedral parameter (B/C I duplicated this set during the process of opt- torsions). For example I have the following duplicated form in my ff output files:
>
> C6 C7 C8 O5 0.6670 1 0.00
> C6 C7 C8 O5 0.7860 3 0.00
>
> My question is which one of these dihedral will be used by MD engine. Or should I remove one of them from my final ff file? If so which one has to be removed?
>
> any suggestions are welcome.
>
> Ehsan.
>