[gmx-developers] inner loop and lennard-jones

Daniele Bemporad DANIELE at biop.ox.ac.uk
Thu May 1 11:03:18 CEST 2003

Hi all.
Thank you very much to David for the quick answer. Re-reading my e-mail 
now, I'm realizing I hasn't been very clear.
The fact is that I need to apply a 4-8 potential between certain pairs of 
atoms (namely between receptor and ligand) and standard 6-12 for all the 
other interactions (ligand-ligand, receptor-receptor, ligand-water, 
receptor-water, water-water). So I cannot define a unique potential. I 
was thinking of going into the subroutine which calculates the 
lennard-jones and put there an "if" statement: if (atom_number of the 2 
atoms involved is between this and that value) then apply 4-8 pot, else 
apply 6-12. That's why I presume I cannot use the -table option. Please 
correct me if I'm wrong.
To test the code I have a simple system with 2 aminoacids in vacuum. 
I'm using a very large cutoff to be sure that all atom-pairs between 
the 2 aminoacids have an interaction. As I said, the only inner loop which 
seems to be involved is the inl3300. But only the 1-4 interactions are 
printed out (both lennard jones and coulomb). Is it correct that in this 
case inl330 is involved? Reading its header, it seems so. But I cannot 
succeed in finding where the other non-bonded interactions are 
calculated. Any suggestions?
Thanks again
Daniele Bemporad

On 30 Apr 2003, David wrote:

> On Wed, 2003-04-30 at 19:37, Daniele Bemporad wrote:
> > Hi all.
> > I need to hack the gromacs code and modify the lennard-jones potential. I 
> > have added print statements in each inner loop to see which of them was 
> > involved in my simulation and to check the value of relevant variables. 
> > In particular, it has turned out that the inner loop involved is the 
> > inl3300. However, only the 1-4 interactions are printed out and there is 
> > no way to find where and when the other non-bonded interactions are 
> > calculated. Can anybody be of any help?
> are you aware of the table potentials?
> Otherwise Erik l. is very busy hacking the code such that it will be
> easier to roll your own loop (pun intended).
> > www interface or send it to gmx-developers-request at gromacs.org.
> -- 
> Groeten, David.

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