David Mobley wrote:
Itamar,
But if the charge weren't neutralized, the electrostatic energy would
be infinite, since an infinite lattice of charged unit cells has
infinite charge and hence infinite interaction energy. (So the trivial
check, of course, is to see whether the energy is infinite if you run
with a charged system. The answer is no).
In PME there are charge and dipole corrections.
With cut-offs it doesn't matter.
David
On 3/31/06, Itamar Kass <[EMAIL PROTECTED]> wrote:
Shalom Bob,
First GROMACS does not nutrelize the charge it will run the system as is, you
have to nutrelzie it manually.
I know this was discussed few weeks ago, please search the mailiong list.
good work, Itamar.
Quoting Bob Johnson <[EMAIL PROTECTED]>:
Hello everyone,
I am using PME to handle electrostatics. What happens if I run a simulation
with
a non-zero net charge? Does GROMACS automatically provide some sort of
background charge to neutralize the system?
Thanks,
Bob Johnson
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| Itamar Kass
| The Alexander Silberman
| Institute of Life Sciences
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________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
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