[AMBER] Periodic boundary conditions and N_OF_BONDS_COLVAR

From: Hugo Macdermott-Opeskin <hugomacdermott.gmail.com>
Date: Wed, 13 Jun 2018 11:51:01 +1000

Dear All

I have been having some trouble trying to run a set of simulations
involving the coordination number of water with an ion using ABMD and the
N_OF_BONDS colvar from nfe_colvar.f90.
I noticed a significant disagreement with values that I computed from the
trajectory using a python script and those output by the ABMD code. I then
delved into the code and found that the N_OF_BONDS colvar does not compute
distances using PBCs. This would normally not be a problem however as water
can move quickly over the PBC, an incorrect ( as far as I can tell) value
is obtained. Has anyone else had this problem?

I have a fix for this using a number of functions written into
nfe_colvar.F90 and some I have written myself, but they are pretty ugly
and am I am struggling to validate my code.
Any help or suggestions would be greatly appreciated.
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Received on Tue Jun 12 2018 - 19:00:02 PDT
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