[AMBER] How to appropriately replace the amber force in the source codes ?

From: jinfeng liu <jinfengliu1119.gmail.com>
Date: Wed, 6 Jan 2016 21:37:46 +0800

Dear Amber source codes authors,

         I want to use amber14 to perform protein MD simulation, but using
the atomic forces calculated in my method. So, I want to modify the Amber
source codes to replace the Amber MM forces with my calculated forces, and
still use the Amber thermostat. I did a little modifications in runmd.F90,
which is in AmberTools/src/sander directory. Specifically, just before

  ! ---Step 1c: do randomization of velocities, if needed:

  ! ---Assign new random velocities every Vrand steps, if ntt=2

I added several lines new codes to replace the Amber MM forces in f() array
with my own calculated forces, like the following:

        do i = 1 , natom
           f(3*i-2) = f2(i,1)
           f(3*i-1) = f2(i,2)
           f(3*i) = f2(i,3)

and f2() array is my calculated force.

I'm not sure whether the above modification is right, and where does Amber
add the heat bath (I think it is in Step 1c region, so I added the
modification just before Step 1c) ?

I am looking forward to your responses, and thanks very much !


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Received on Wed Jan 06 2016 - 06:00:05 PST
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