From: Nathan A. Baker <baker@ch...> - 2004-07-27 13:20:42
Hi Sekwan --
Yes; this makes sense -- we did something very similar in:
Lin JH, Baker NA, McCammon JA. Bridging implicit and explicit
solvent approaches for membrane electrostatics. Biophys. J. 83,
One thing that was important in that simulation was the padding of the
calculation box with periodic copies.
Of course, the ideal way to calculate electrostatics would be with the
PME routines used in the simulation -- however, I'm not sure how to do
this with most codes.
Numerical Poisson solvers are good choices for these types of
calculations because they do not generate infinite potential values
near "point" charges -- a problem you would encounter with simple
application of Coulomb's law. These infinite values are usually in
uninteresting regions of the system (e.g., inside water molecules) and
are typically integrated out over the course of the trajectory.
Sekwan Oh <ohsk75@...> (07-26-2004 13:46:56-0700):
>Dear professor Baker,
>I am trying to run MD simulation using Gromacs which so far has been able
>for explicit water systems.
>However I would like to calculate the electric potential of the system after
>the MD is done.
>Does it make sense to use APBS(implicit solvent) for electric potential
>analysis using the data from the MD(using explicit waters).
>The reason why I'm using Gromacs is my system of interest uses periodic
>Are there any programs to calculate electric potential for explicit water
>system? Or, is the implicit PB scheme only solution to obtain electric
>Thank you so much professor Baker!
End of message from Sekwan Oh.
Nathan A. Baker, Assistant Professor
Washington University in St. Louis School of Medicine
Dept. of Biochemistry and Molecular Biophysics
Center for Computational Biology
700 S. Euclid Ave., Campus Box 8036, St. Louis, MO 63110
Phone: (314) 362-2040, Fax: (314) 362-0234
PGP key: http://cholla.wustl.edu/~baker/pubkey.asc