[gmx-users] Define: Energy groups

[Tsjerk Wassenaar]

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