[gmx-users] Define: Energy groups

[Xavier Periole]

On Fri, 13 Jun 2008 02:46:16 +0530 (IST)
  tuhin at iitk.ac.in wrote:
> Dear Tsjerk,
> 
> Actually, I have defined the groups for Temp-coupling as:
> 
> tc-grps             =  Protein_CA2+ SOL
> 
> Thus, I felt would I be incorporating any errors, if I define my
> energygrps as:
> 
> energygrps          =  Protein SOL
> 
> I have generated my index.ndx file exactly the way you defined
> (Protein_CA2+) and supplied it to the grompp.
"energygrps" ONLY defines groups for which the energies will be
stored in the output (ener.edr) for you to access them easily
with g_energy.

The definition of energygrps will in no manner affect the way the
interaction energies are calculated in the propagation of the
program, when you run mdrun. They are actually not used, forces
are.

XAvier
> 
> Thanks for your valuable time.
> 
> Regards,
> Tuhin
> 
> 
>> Hi Tuhin,
>>
>> It depends on what you do. In both cases you will have to run grompp
>> with an index file with a group specified, containing both the Protein
>> and the calcium ion. You can take an existing index file (created
>> simply with "echo q | make_ndx -f mystructure.gro") and add the number
>> of the calcium ion under the label [ Protein ] or you make the
>> combination within make_ndx, combining the two groups. In the later
>> caseyou're likely to end up with a group called Protein_CA2+. Key
>> issue to understand is that it's not sufficient to only define a group
>> in the .mdp file. Except for the standard groups gromacs knows, a
>> group will have to be defined through an index file.
>>
>> Cheers,
>>
>> Tsjerk
>>
>> On Thu, Jun 12, 2008 at 10:08 PM,  <tuhin at iitk.ac.in> wrote:
>>> Dear Mark,
>>>
>>> To continue further, do I need to define my "energy groups" as:
>>>
>>> energygrps          =  Protein_CA2+  SOL
>>>
>>> OR, I could do as:
>>>
>>> energygrps          =  Protein  SOL
>>>
>>> Best,
>>> Tuhin
>>>
>>>
>>>
>>>  tuhin at iitk.ac.in wrote:
>>>> Dear Gromacs users,
>>>>
>>>> My protein is a heterodimer (a small chain:A and a large chain:B). A
>>>> single Ca2+ ion is found interacting with residues from chain:B only.
>>>> In
>>>> the .pdb file the Ca2+ is assigned a chain:B identifier.
>>>>
>>>> HETATM 6504 CA   CA  B1579      23.021 -16.233   6.204  1.00  7.96
>>>>  CA
>>>>
>>>> When I visualize the protein and generate a conolly surface, I could
>>>> see
>>>> the Ca2+ ion completely buried within chain:B. Now, I have two
>>>> questions:
>>>>
>>>> 1. I would like to perform an MD on the above protein using Gromacs
>>>> 3.2.1
>>>
>>>  Unless you have a really good reason (e.g. compatibility with old
>>>  results), you should be planning to use a more recent version.
>>>
>>>> suit with ffG43a1 forcefield. I know the Ca2+ ion is not accessible to
>>>> solvent molecules. Will the forcefield parameter for Ca2+ sufficient
>>>> enough to take this fact into account. I mean, Ca2+ in solvent and Ca2+
>>>> in
>>>> protein; for both the cases could I use the Ca2+ with +2 charge ? What
>>>> about the vdw contribution between the interacting residues from
>>>> chain:B
>>>> and Ca2+ ion ?
>>>
>>>  To answer that, you should read about how these parameters were
>>>  developed for the force field. Perhaps you will need to refine them
>>>  yourself - but this is not a good thing to do early in your MD and/or
>>>  GROMACS experience.
>>>
>>>> 2. When defining groups for Temp-coupling; could I do something like
>>>> (as
>>>> I
>>>> know the Ca2+ not accessible to solvent):
>>>>
>>>> tc-grps             =  Protein_CA2+ SOL
>>>
>>>  That would be reasonable and effective.
>>>
>>>  Mark
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>>
>>
>>
>> --
>> Tsjerk A. Wassenaar, Ph.D.
>> Junior UD (post-doc)
>> Biomolecular NMR, Bijvoet Center
>> Utrecht University
>> Padualaan 8
>> 3584 CH Utrecht
>> The Netherlands
>> P: +31-30-2539931
>> F: +31-30-2537623
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> 
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-----------------------------------------------------
XAvier Periole - PhD

NMR & Molecular Dynamics Group
University of Groningen
The Netherlands
http://md.chem.rug.nl/~periole
-----------------------------------------------------