[gmx-developers] PME error with implementation of new bonded interaction function

[Maarten Wolf]

Dear all,

I sent this message again because I noticed it ended up in the wrong
thread. What I forget to mention in the first message is that I will
already be helped when anyone can direct me to a manual of some sort on
implementing a new bonded interaction function.

I recently implemented an extra bonded function into gromacs 3.3.1, and
everything worked correctly (at least that is what I thought) when I
used Cut-off or Reaction Field.

But when I switched to PME it all went wrong. I initially got a
segmentation fault after the first step. This was caused by the pme
routine that changed one of the static pointers in the lincs algorithm.
switching from fftw2 to fftw3 seemed to do the trick, but after some
simulations I noticed that although I do not get a segmentation fault
anymore I can not reproduce my results. This is still linked to the pme
routine, since the usage of other coulombtype gives reproducable
results.

Maybe I made some error in the implementation therefor here the list
what I did:
add  t_ifunc in bondf.h
add  F_FUNCT in F_NRE enum in idef.h
add  t_iparams struct in idef.h
add  eNR_FUNCT in eNRNB in nrnb.h
add  def_bonded definition in t_interaction_function in ifunc.c
add  my own function in bondfree.c
add  estimated flop in t_nrnb_data in nrnb.c
add  parameter io in tpxio.c

If I am missing some point that has its influence on the PME routine,
please let me know. Or any other suggestions.

Thanks in Advance,
Sincerely,
Maarten Wolf



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