[gmx-users] Define: Energy groups

[tuhin at iitk.ac.in]

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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