[gmx-developers] ensemble code and restraints

[David van der Spoel]

Erik Lindahl wrote:
> Hi,
> 
> Robert probably knows better than I, but what I was thinking of is that 
> you can consider the cRMS a potential and derive it analytically to get 
> "forces", which you then apply to the atoms with some arbitrary factor 
> to control the strength of the restraint.
Somewhat off-topic, but with the genrestr program you can generate a 
matrix of distance restraints (based on an index file) and you can 
restrain internal motions (but not overall translation and rotation).
> 
> Cheers,
> 
> Erik
> 
> On Dec 8, 2008, at 9:37 AM, hessb at mpip-mainz.mpg.de wrote:
> 
>> Hi,
>>
>> What do you mean with exactly with RMSD restraint?
>> Why would you want to keep the molecules aligned?
>>
>> Sub ensembles are not implemented.
>> I guess the easiest way to implement this would be
>> to give certain zero weights to restraints in certain samples.
>> Note that because of the 1/r^6 averaging, a pair in one molecule
>> that is at larger distance than the shortest pair
>> is effectively not restrained.
>>
>> Berk
>>
>>> OK that sounds great, I will wait for this and in the mean time work
>>> on my second question. Can someone tell me, maybe Berk knows best, if
>>> there is a simple RMSD restraint in GROMACS over an ensemble. I would
>>> like to keep all the molecules aligned during the simulation.
>>>
>>> Also can one select sub samples of the ensemble over which distance
>>> restraints are applied?
>>>
>>> Thanks for the help regarding force fields,
>>>
>>> Bryn
>>>
>>>
>>> 2008/12/8 Erik Lindahl <lindahl at cbr.su.se>:
>>>> Hi,
>>>>
>>>> Please contact Pär Bjelkmar (bjelkmar at cbr.su.se) if you need a charmm
>>>> port;
>>>> starting with gromacs 4.0.2 (or something like that, but it's in the
>>>> release
>>>> branch) there is code in  pdb2gmx and grompp to correctly work with the
>>>> multiple torsions terms used in Charmm.
>>>>
>>>> The force field files will be added to CVS shortly too, but we'd 
>>>> love to
>>>> have a "complete" version including CMAP before pushing it out into the
>>>> world to avoid confusion  (that's also the only reason why we'd like 
>>>> Pär
>>>> to
>>>> have a list of people using the preliminary version)
>>>>
>>>> Cheers,
>>>>
>>>> Erik
>>>>
>>>>
>>>> On Dec 8, 2008, at 3:54 AM, Mark Abraham wrote:
>>>>
>>>>> Daniel Larsson wrote:
>>>>>>
>>>>>> On Dec 7, 2008, at 11:15 , Robert Fenwick wrote:
>>>>>>>
>>>>>>> Hi,
>>>>>>>
>>>>>>> I have two questions.
>>>>>>>
>>>>>>> Firstly are the AMBER (99SB) and CHARMM (CMAP) force fields full
>>>>>>> integrated in GROMACS 4.0?
>>>>>>
>>>>>> If you are interested to use the Amber force field with Gromacs, this
>>>>>> page is a most valuable resource:
>>>>>> http://chemistry.csulb.edu/ffamber/
>>>>>> It is a port of the force field which originally was made for the
>>>>>> Folding at Home-project.
>>>>>> When it comes to the Charmm force field, I'm not aware of any good
>>>>>> port.
>>>>>
>>>>> Well there is a CHARMM port or two (I wrote a partial one; it's in the
>>>>> contributions section of the GROMACS webpage) but invoking it is
>>>>> trickier
>>>>> than with other forcefields because of quirks in CHARMM and 
>>>>> limitations
>>>>> of
>>>>> grompp.
>>>>>
>>>>> Mark
>>>>> _______________________________________________
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>>>>
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>>
>>
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-- 
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se