[gmx-users] short and long range coulomb with pme
Jose D Faraldo-Gomez
jdfg_gmx at hotmail.com
Wed May 1 11:14:57 CEST 2002
>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.
And would this Ca-Ca energy be positive or negative? We've tried this
workaround for a Water+8Na+8Cl system (using gmx2) and although both the SR
and LR energies of the reduced systems (some of which are charged) add up
almost exactly (as exactly as LJ does) to that of the whole system (which is
neutral), the values of the energies for e.g. LR Na-Na and LR Cl-Cl are
negative (-410 and -408 KJ/mol).
How do you interpret this result? In other words, if using this workaround
one gets pairwise PME energies which are so unphysical (e.g. for ion-ion),
how to be sure one that the others are right (e.g. water-ion or protein-ion)
or at least that can be compared with e.g. cut-off energies? Have you
addressed this in your manuscript?
Thanks once more,
Chat with friends online, try MSN Messenger: http://messenger.msn.com
More information about the gromacs.org_gmx-users