[gmx-developers] ensemble code and restraints

[Robert Fenwick]

OK I am still a bit lost about the restraining of distance restraints
over pairs of structures within an ensemble. I have looked at the
manual and it seems that what I would like to do is indeed ensemble
averaging over pairs. How is it possible to specify which replicas are
involved? I essentially want to treat these pairs as dimers, so that
there is only a force on the molecules if both structures in a pair do
not fulfill a distance restraint.

The system suggested by Richter et al. is a chain loop, i.e. pairs of;
1 and 2, 2 and 3, 3 and 4, 4 and 1

Cheers,


Bryn



2008/12/9  <hessb at mpip-mainz.mpg.de>:
> Hi,
>
> You can select any group in the molecule for determining the matrix R.
> The orientation of molecules is never restrained.
> I still don't see why you want to do that.
> Once you have the matrix R, you can apply any restraints
> on the rotated system, without rotating back the system.
> That all there is.
> You will have to code something yourself if you want to do more.
> I guess you can do most things you want when you have access to R.
>
> Berk
>
>> OK I have almost found the thing that I want except there is one snag,
>> it is not as flexible as I would like it to be. In the manual in the
>> orientation description this appears:
>>
>> For reasons which are explained below, the D matrices are calculated
>> which respect to a reference orientation of the molecule. The
>> orientation is defined by a rotation matrix R which is needed to
>> least-squares fit the current coordinates of a selected set of atoms
>> onto a reference conformation. The reference conformation is the
>> starting conformation of the simulation. In case of ensemble
>> averaging, which will be treated later, the structure is taken from
>> the first subsyste.
>>
>> would it be possible to define the RMS restraint in this way first
>> calculating the rotation matirx R and then applying it? Then derriving
>> forces based on the rmsd to the average structure? Also would it be
>> possible to define the selection of atoms required for this
>> least-squares fitting? I would like to just apply the restraint to the
>> secondary structures of my system.
>>
>> Cheers,
>>
>>
>> Bryn
>>
>>
>>
>>
>> 2008/12/8 Robert Fenwick <robert.fenwick at irbbarcelona.org>:
>>> 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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