[gmx-users] criticism invited...

[Eric Jakobsson]

Another approach would be to use a higher mass for that hydrogen.

At 10:38 AM 3/21/2003 +0000, you 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?
>
>many thanks
>
>Paul
>_______________________________________________
>gmx-users mailing list
>gmx-users at gromacs.org
>http://www.gromacs.org/mailman/listinfo/gmx-users
>Please don't post (un)subscribe requests to the list. Use the
>www interface or send it to gmx-users-request at gromacs.org.

---------------------------------
Eric Jakobsson, Ph.D.
Professor, Department of Molecular and Integrative Physiology, and of 
Biochemistry
Senior Research Scientist, National Center for Supercomputing Applications
Professor, Beckman Institute for Advanced Science and Technology
4021 Beckman Institute, mc251
405 N. Mathews Avenue
University of Illinois, Urbana, IL 61801
ph. 217-244-2896       fax 217-244-2909