[gmx-developers] ensemble code and restraints

[Erik Lindahl]

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.

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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