[gmx-users] converting ILDN parameters to RB

[David van der Spoel]

On 2011-03-31 15.27, Alan Wilter Sousa da Silva wrote:
> Hi there,
>
> Since ILDN dihedrals has some parameters with up to periodicity 6, I was
> wondering if it's possible to convert it in RB with 6 coefficients. If
> so, what would be the formula? For example, for converting the usual
> Amber99SB to RB I have:
ILDN is already supported in the latest gromacs releases, by simply 
using multiple proper dihedrals. Why would you want to change it?

>
> if phase in [0, 180]:
>
> if kPhi > 0: V[period] = 2 * kPhi * cal
>
> if period == 1:
>
>                          C[0] += 0.5 * V[period]
>
> if phase == 0:
>
>                              C[1] -= 0.5 * V[period]
>
> else:
>
>                              C[1] += 0.5 * V[period]
>
> elif period == 2:
>
> if phase == 180:
>
>                              C[0] += V[period]
>
>                              C[2] -= V[period]
>
> else:
>
>                              C[2] += V[period]
>
> elif period == 3:
>
>                          C[0] += 0.5 * V[period]
>
> if phase == 0:
>
>                              C[1] += 1.5 * V[period]
>
>                              C[3] -= 2 * V[period]
>
> else:
>
>                              C[1] -= 1.5 * V[period]
>
>                              C[3] += 2 * V[period]
>
> elif period == 4:
>
> if phase == 180:
>
>                              C[2] += 4 * V[period]
>
>                              C[4] -= 4 * V[period]
>
> else:
>
>                              C[0] += V[period]
>
>                              C[2] -= 4 * V[period]
>
>                              C[4] += 4 * V[period]
>
>
> So, as you can see, I can handle up to 4 periods (C[5] is always 0, but
> not with ILDN and I need to add C[6] rules as well).
>
> Any ideas? Many thanks in advance,
>
> Alan
> --
> Alan Wilter SOUSA da SILVA, DSc
> Bioinformatician, UniProt - PANDA, EMBL-EBI
> CB10 1SD, Hinxton, Cambridge, UK
> +44 1223 49 4588
>


-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se