[gmx-users] short and long range coulomb with pme

David van der Spoel spoel at xray.bmc.uu.se
Wed May 1 12:38:18 CEST 2002

On Wed, 1 May 2002, Jose D Faraldo-Gomez wrote:

>>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?
No I haven't, but I only had neutral molecules.

Your results are puzzling, but I suggest you check the charge correction
in the PME algorithm that I wrote about before (see

Groeten, David.
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

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