[gmx-users] criticism invited...

[Paul Barrett]

Hi

I would welcome any opinions on the validity of a fix I have just
implemented in an MD run.

The problem: when simulating a globular protein with a docked ATP
molecule a terminal ATP hydrogen spins about its oxygen at > 3 cycles
per femtosecond. I can stabilise the simulation by running it with a
timestep of 0.1 fs but this is not practical for a real run.

My (alledged) solution: combine this hydrogen with its neighbouring
oxygen by:

1) make a new dummy atom in ffgmx.atp file to represent the OH group as
a single atom with mass = sum of components.
2) modify ffgmx.rtp for ATP to remove the hydrogen and turn the Oxygen
in to the OH blob with a charge = sum of components.
3) modify my pdb file to remove the hydrogen

Im not crucially interested in the hydrogen: I want to look at global
movements of the the protein.

Is this a legitimate approach?
Would you recommend a better way?

many thanks

Paul