[gmx-users] short and long range coulomb with pme
David van der Spoel
spoel at xray.bmc.uu.se
Tue Apr 30 00:02:04 CEST 2002
On Mon, 29 Apr 2002, Erik Lindahl wrote:
>No, the problem is that it isn't possible to separate group
>contributions in the PME algorithm. I'm pretty sure it says that
>somewhere in the manual too :-)
Actually I just submitted a manuscript with a workaround. The trick is
quite simple, you use tpbconv to make one group, e.g. the Ca++ have zero
charge, and the you use the mdrun -rerun option to rerun your trajectory.
Now you will get the PME energy for SOL-SOL. If you have multiple ions,
you can then set the charges of the solvent to 0 and mdrun -rerun again.
That will give you the PME energy for Ca-Ca.
Now the interaction energy Ca-SOL is the difference between the original
PME energy and that from the two reruns.
Dr. David van der Spoel, Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576, 75123 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://zorn.bmc.uu.se/~spoel
More information about the gromacs.org_gmx-users