On Fri, Apr 5, 2013 at 9:50 PM, kurisaki <
kurisaki.ncube.human.nagoya-u.ac.jp> wrote:
> Dear Amber developers and users,
>
> I'd like to calculate force acting on each atoms
> By using MD trajectory I already got.
>
> I guess "runmd.f90" should be changed to realize the purpose.
>
> And, for the purpose, I want to use sander with IMIN=5 but
> Have not a concrete idea to how modify the source code yet.
>
You will need to use the "runmin.F90" source file instead of runmd if you
plan on using imin=5.
The runmd() subroutine is only called for running dynamics.
>
> In "runmd.f90", I found
> (1) forces are calculated in "Step 1b" by using "force module"
> And values are put into "f"
> (2) trajectory, velocity and restart files are written in
> "Step 5", where some flags are monitored, e.g. ntwr.
>
> Then, I am wondering that I should give some statements
> To write "f" as force in "Step 5".
>
> However, I also am wondering that I have to set additional frag
> And parameters such line "ntwf" for setting the interval to write down
> force.
>
This variable does not exist. You would have to add it manually (or you
could just hard-code the force printing routine for your particular
application).
The 'f' variable in the force() call will contain the forces after they
come back from that subroutine. You would then have to print out these
variables the way you want them.
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Fri Apr 05 2013 - 21:00:02 PDT
