[gmx-users] Define: Energy groups

[tuhin at iitk.ac.in]

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.

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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