[gmx-developers] energy calculation

[Vibin R]

Dear Sir,

   I have been trying to figure out the routine mcinl1100 in the gromacs
package, version 3.1  Could you be kind to let me know in which code
this loop is situated. I have searched almost all the relevant codes. 

Sincerely
Vibin R.




> Date: Thu, 07 Mar 2002 16:11:04 +0530
> From: Erik Lindahl <lindahl at stanford.edu>
> To: Vibin R <vinu at btc.iitb.ac.in>
> Cc: gmx-developers at gromacs.org
> Subject: Re: [gmx-developers] energy calculation
> 
> 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
> 
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