[gmx-developers] energy calculation

[Erik Lindahl]

Vibin R wrote:

>Dear Sir,
>
>  This is in refrence to an earlier correspondence you had with me. I am
>enclosing the mail for your refrence. 
>
>The problem I am facing in using the wrapper is that the programme
>calc_enery.c seems to be incomplete. It defines a function mcinl1100 but
>does not have what actually that function is.
> Could you please throw some light on how the wrapper is to be used. It
>shall be of immense help to me. I am currently working on various
>optimization adaptations of the dead end elimination algorithm with a goal
>towards automated protein design. I want to incorporate GROMACS to calculate
> the pairwise interaction energies for the protein side chains and also
>the interaction energy of a side chain with the amino acid backbone.
>
>Looking forward to an encouraging response,
>
>Sincerely 
>vibin
>

Hi Vibin,

"Wrapper" just means that it is a small shell function which in turn 
calls another function that does the actual work.

In this case, mcinl1100 is one of the inner loops in the gromacs 
package, so you have to compile and link with the gromacs library. (mc 
stands for monte carlo, meaning we do not calculate forces in this loop, 
only potential).

You can of course work directly with mcinl1100 - the only reason to use 
the wrapper is that it might be slightly better documented and has fewer 
options...

Erik