[gmx-developers] inner loop and lennard-jones
DANIELE at biop.ox.ac.uk
Thu May 1 11:03:18 CEST 2003
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?
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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