[gmx-developers] ensemble code and restraints
robert.fenwick at irbbarcelona.org
Mon Dec 8 18:13:29 CET 2008
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 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)
> 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, this
>>> 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 the
>> contributions section of the GROMACS webpage) but invoking it is trickier
>> than with other forcefields because of quirks in CHARMM and limitations of
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