Dear Mr. Swails
Thank you for kind support and encouraging me.
> You will need to use the "runmin.F90" source file instead of runmd if you
> plan on using imin=5.
All right..I must modify "runmin.F90".
Actually, "sander.F90" use "runmin.F90"
When "trajene.F90" is called under "imin = 5".
Now it might be alternative way to modify "trajene.F90"
to give force information.
I expected that I can get force and energy all together,
without adding new frags and parameters.
Then, I have an idea to modify "trajene.F90" as below.
1) After "call runmin",
add a statement, "call force".
2) then, write the force information
With mdcrd-like format
Does this procedure work?
I really appreciate if you give some advices
Or more useful/practical alternatives.
Yours sincerely,
Ikuo KURISAKI
PS:
I am just confused because "f" is defined as energy
in "runmin.F90" (see Line 297 in the source code)
Where can we find values obtained from "call force"?
I mean what variable should be assigned to write
Force information.
-----Original Message-----
From: Jason Swails [mailto:jason.swails.gmail.com]
Sent: Saturday, April 06, 2013 12:34 PM
To: AMBER Mailing List
Subject: Re: [AMBER] How to modifie "runmd.f" to calculate force from obtained
MD trajectory?
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 Sat Apr 06 2013 - 22:00:07 PDT
