# Re: Calculating electrostatic force from NAMD trajectory

From: sunyeping (sunyeping_at_aliyun.com)
Date: Mon Jul 03 2017 - 21:42:56 CDT

Hi,
I use the vmd plugin "NAMD energy" to calculate the electrostatic force of the selected atoms. Do you think this is apt for your purpose?
All the best.
Yeping Sun------------------------------------------------------------------From:Ben Lowe <ben.lowe.uk_at_googlemail.com>Time:2017 Jul 4 (Tue) 10:37To:namd-l <namd-l_at_ks.uiuc.edu>Subject:namd-l: Calculating electrostatic force from NAMD trajectory
I'm interested in calculating the electrostatic-only force on an atom
within my system at every frame of a completed trajectory. The
application is calculating the electric field on a test charge.

The simulation was ran using PME for electrostatics with the EW3DC
correction applied via the 'extforces' module, so ideally the
resulting force would include both these, but a simple nearest
neighbor coulombic sum may also be acceptable as an approximation to
this.

Does anyone know what would be an efficient way to calculate the
electrostatic-only force on an atom for many (i.e. several thousand)
frames?

I can imagine the brute force way would be to write out every frame
into a pdb/psf, and then run a separate NAMD 'minimisation' for every
frame with the following settings:

cutoff 0.1 # essentially disable VDW interactions
binaryoutput off ;
run 0
output onlyforces \$outputname

But I'm sure there is a more efficient way; for example can tclforces
be used for this kind of post-processing
analysis?(http://www.ks.uiuc.edu/Research/namd/2.9/ug/node50.html)

Or colvars maybe
(http://www.ks.uiuc.edu/Research/namd/2.9/ug/node55.html#SECTION000132230000000000000)
but this seems to be aimed at ABF calculations rather than this more
simple problem.

Thank for any suggestions,

Ben

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