VMD-L Mailing List
From: Michael LeVine (mlevine_at_wesleyan.edu)
Date: Tue Sep 12 2017 - 09:37:30 CDT
- Next message: Shivanand Malaganvi: "Unable to visualize the solid isosurfaces"
- Previous message: John Stone: "Re: intel_do_flush_locked failed: Cannot allocate memory"
- Next in thread: John Stone: "Re: Electrostatic interaction calculations using the NAMD Energy Plugin and PME"
- Reply: John Stone: "Re: Electrostatic interaction calculations using the NAMD Energy Plugin and PME"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]
Hi all,
I am calculating the non-bonded interaction energy between an ion and its
coordinating residues over the course of a simulation using the NAMD Energy
Plug-in. While NAMD Energy has the option to use PME in the calculation,
which we used during our simulations, it is not clear to me how the plug-in
is calculating the portion of the long-range electrostatic interaction. It
is my understanding that once using PME, the long-range electrostatic terms
can't be trivially decomposed. Is the plug-in only outputting the
short-range interaction terms?
Thanks,
Michael
-- Michael V. LeVine, PhD Institute Fellow, Institute for Computational Medicine Instructor in Physiology and Biophysics Instructor in Computational Biomedicine Department of Physiology and Biophysics, Weill Cornell Medicine
- Next message: Shivanand Malaganvi: "Unable to visualize the solid isosurfaces"
- Previous message: John Stone: "Re: intel_do_flush_locked failed: Cannot allocate memory"
- Next in thread: John Stone: "Re: Electrostatic interaction calculations using the NAMD Energy Plugin and PME"
- Reply: John Stone: "Re: Electrostatic interaction calculations using the NAMD Energy Plugin and PME"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]