AMBER Archive (2004)

Subject: RE: AMBER: user force

From: Ross Walker (
Date: Thu Jul 22 2004 - 17:40:16 CDT

Dear Myunggi.

Assuming you already know fortran 90 your best bet is to compile the amber
code with debug flags -g and then follow the code slowly using a debugger.
In this way you can see how it branches etc. Most of the work is done in
force.f and ene.f these are the ones you will have to add your new energy
function and differential (force) to. It is essential that the energy and
force for your new function are in sync or you will get minimisation
problems and problems conserving energy in MD. You will also need to modify
the routines that read in the prmtop file so that they read in the
parameters for your new function. Alternatively if it is a one off
calculation you could hard wire the parameters etc into the force and energy
routines and so avoid needing to modify the prmtop reading routines. If you
are fluent in Fortran it should be fairly easy to follow what is going on. I
know the comments in the code are fairly scarce but after a bit of trial and
error you should be able to see how things work.

If you are not fluent in Fortran then you have a long road ahead of you. Try
starting with a good intro to fortran. There are many many different books
out there, all as good as each other, that will introduce you to programming
in fortran.

All the best

|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- |
| | PGP Key available on request |

> -----Original Message-----
> From:
> [] On Behalf Of
> Sent: 22 July 2004 15:26
> To:
> Subject: RE: AMBER: user force
> Thank you Ross Walker.
> If it is the only way to modify(add my own function) the
> source file and
> recomrile, would you recommend any refference or information?
> --
> Best wishes,

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