[gmx-users] short and long range coulomb with pme
David van der Spoel
spoel at xray.bmc.uu.se
Wed May 1 02:56:17 CEST 2002
On Tue, 30 Apr 2002, Jose D Faraldo-Gomez wrote:
>>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.
>But I thought that having a non-zero net charge in PME calculations wasn't a
>good idea... I mean, would the electrostatic energies be additive if one
>goes from a system that is originally neutral to a number of reduced
>subsystems which aren't?
Good point. That depends on whether charge and dipole corrections are
used. When these are turned off in all cases it should be additive...
The charge correction can not be turned off in the current implementation,
the dipole correction is off when the epsilon_surface = infinity (write
inf or 0 in mdp file). The charge correction (see ewald_util.c) is
vc = -qsum*qsum*M_PI*ONE_4PI_EPS0/(2.0*vol*ewc*ewc);
So if your total charge changes as a result of taking a subsystem, some
extra bookkeeping is necessary.
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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