[gmx-developers] ensemble code and restraints

[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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