[gmx-users] criticism invited...

[David van der Spoel]

On Fri, 2003-03-21 at 11:38, Paul Barrett wrote:
> 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?

yes, add a small dihedral potential to the P-O bond. Also, if the
hydroxyl group were hydrogen bonded this would not happen. With
constraints and the dihedral you would be able to use time steps of 2
fs. Check dihedral potentials for e.g. Ser and THr residues for
parameters.
> 
> many thanks
> 
> Paul 
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-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell & Mol. Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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