[gmx-users] converting ILDN parameters to RB

[Alan Wilter Sousa da Silva]

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 <spoel at 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.
> spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
> --
> gmx-users mailing list    gmx-users at 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-request at 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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110331/b9bc745d/attachment.html>