I know it's supported. I was just investigating the possibility since I build acpype to create topologies for gromacs, but also it converts from amber to gromacs (like amb2gmx.pl), and so I was wondering about RB with 6 coefficients since multiple proper dihedrals is only supported for gmx 4.5 and above.
But I don't want to fuss about it. If to forget about GMX 4.0.x and below is the way, so it will be. Thanks, Alan On 31 March 2011 16:08, David van der Spoel <sp...@xray.bmc.uu.se> wrote: > 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. > sp...@xray.bmc.uu.se http://folding.bmc.uu.se > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Alan Wilter SOUSA da SILVA, DSc Bioinformatician, UniProt - PANDA, EMBL-EBI CB10 1SD, Hinxton, Cambridge, UK +44 1223 49 4588
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