[gmx-users] Define: Energy groups
tuhin at iitk.ac.in
tuhin at iitk.ac.in
Thu Jun 12 22:08:12 CEST 2008
To continue further, do I need to define my "energy groups" as:
energygrps = Protein_CA2+ SOL
OR, I could do as:
energygrps = Protein SOL
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
> 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
> 1. I would like to perform an MD on the above protein using Gromacs
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+
> 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
> 2. When defining groups for Temp-coupling; could I do something like (as
> know the Ca2+ not accessible to solvent):
> tc-grps = Protein_CA2+ SOL
That would be reasonable and effective.
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