[gmx-developers] ensemble code and restraints
lindahl at cbr.su.se
Mon Dec 8 18:36:42 CET 2008
We don't have direct RMSD/cRMS restraints, partly because it would be
costly to calculate on-the-fly in parallel runs, but there are some
pretty advanced ways in which you can apply distance restraints in
molecules (also ensemble-based ones) in order to maintain your cRMS.
It's described in detail in the written manual!
On Dec 8, 2008, at 9:13 AM, Robert Fenwick wrote:
> 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,
> 2008/12/8 Erik Lindahl <lindahl at cbr.su.se>:
>> 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
>> 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
>> 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)
>> On Dec 8, 2008, at 3:54 AM, Mark Abraham wrote:
>>> Daniel Larsson wrote:
>>>> On Dec 7, 2008, at 11:15 , Robert Fenwick wrote:
>>>>> 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,
>>>> page is a most valuable resource:
>>>> 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
>>> contributions section of the GROMACS webpage) but invoking it is
>>> than with other forcefields because of quirks in CHARMM and
>>> limitations of
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