[gmx-developers] ensemble code and restraints

[Robert Fenwick]

I would like to implement the method that was described in Richter et
al. 2008. The method that was named MUMO and restrains order
parameters over an ensemble of 16 replicas, while at the same time
restraining NOE data over pairs of structures in the ensemble
(sub-samples). The original code was written in CHARMM and is not
available for general use.

Yes Berk you are right about the r-6 averaging and they show that the
correct averaging in this case is r-3 averaging.

They also use the Lipari-Szabo approximation to derive an order
parameter restraint, I would like to implement as well.

I would like to restrain the RMSD of the backbone as a control for this work.


Bryn


2008/12/8  <hessb at mpip-mainz.mpg.de>:
> 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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