[gmx-developers] ensemble code and restraints

[Robert Fenwick]

I am not up to speed with optimizations of code, however I would have
thought that it was not so computationally intensive to calculate the
average coordinates at each step and then determine velocities based
on the atomic displacements? However I will look at the manual before
I ask more questions.

2008/12/8 Erik Lindahl <lindahl at cbr.su.se>:
> Hi,
>
> 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!
>
> Cheers,
>
> Erik
>
>
>
>
> 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,
>>
>> 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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