[gmx-users] Pairwise Enery Calculation

Manish Gupta manishg at che.iitb.ac.in
Wed Mar 6 11:00:11 CET 2002

Hello All, 
  I am working on a project dealing with implemntaion of the various forms
of Dead End Elimination algorithm. The final goal being automated protein
design. I want to use gromacs for calculation of pairwise interaction
energies of side chains and also the interaction energy of a side chain
with amino acid backbone. I had received a wrapper for the same from
gromacs people which I am enclosing with this mail. 
 Now the problem is, I am unable ot figure out how to use the
wrapper. This seems to be inomplete. It just defines a function mcinl1100
but does not actually code for it. 
 If someone can help me in this regards, it shall be of immense help to
my project.


Manish Gupta
Senior Undergraduate Student
Chemical Engg. Student
IIT Bombay

PS: Below is the earlier correspondence a freind of mine had with gromacs.

> > Dear Sir
> >         Can we calculate the potential energy of a structure from a
> > pdbfile with gromacs, without doing either energy mininisation or MD. If
> > it has to be done with slight adjustments in the source code, please let
> > me know, where the changes has to be made. Basically i want to get the
> > vanderwaals and coulombic interaction energies of a structure from a given
> > pdb file.
> >         Expecting your kind attention
> > Regards
> > vibin
> Hi Vibin,
> Together with Olivia Eriksson in Stockholm I've adapting things slightly to
> be able to use gromacs in monte carlo and sidechain energy simulations. If
> you want to try the CVS version of gromacs (that has monte carlo innerloops
> without forces) you could use the attached somewhat documented wrapper
> function to calculate the coulomb and lennard-jones energies directly. If all
> parameters are in Gromacs units you'll get the energy in gromacs units too.
> However, please note that a pdb structure can have an very high potential
> energy unless you use the same forcefield as the structure was refined with.
> Normally it's a good thing (TM) to do a few steps of energy minimization to
> get around this, but your milage may vary.
> Cheers,
> Erik
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