Hi Rodney,
the other alternative is to define the springs in your topology file.
You first need to merge
your groups (is part of different molecules) and run the different
combination you need by
defining them by hand; you can easily write a awk script to generate
the different topologies
you need.
Then you can use a 2D wham to combine the different histograms you've
obtained and
get your 2D PMF.
XAvier.
On Mar 16, 2009, at 8:28 PM, <rvers...@ccny.cuny.edu> <rvers...@ccny.cuny.edu
> wrote:
Hello everybody:
I am trying to perform some PMF calculations using the pull code
with a spring (umbrella sampling) but using two reaction coordinates
(E1 and E2) between four different groups (r1,r2,r3 and r4).
All the examples and tutorials that I found so far on the web, only
mention PMF calculations for one reaction coordinate (E1) between
two different groups (r1 and r2).
Is it possible to perform the calculations using two reaction
coordinates at the same time or should i do two different individual
calculations or there is something more that i should do to achieve
it?
I will appreciate any help.
-Rodney
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