[gmx-developers] inner loop and lennard-jones

[Daniele Bemporad]

Hi all.
I think I have found my mistake: I was only looking at the .c files and 
missing the .s source code. My fault. Now I get the inner loops right.
Thanks anyway. I'll probably bother you with some other question as they 
come along.
Daniele Bemporad

On Thu, 1 May 2003, Daniele Bemporad wrote:

> 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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