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

[David van der Spoel]

Maarten Wolf wrote:
> 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.
In that case I can point you to the 3.3 pdf manual, because it tells you 
which routines to alter.
> 
> 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.
This is impossible, so I suspect another indirect effect, typical 
unitialized parameters on the stack, or e.g., you declare an array on 
the stack and write outside its border.

  int bla[12];
  bla[14] = -1;


> 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.
> 
see manual, there are a couple more places where stuff needs to be added...


> Thanks in Advance,
> Sincerely,
> Maarten Wolf
> 
> 
> 
> Send instant messages to your online friends http://uk.messenger.yahoo.com 
> _______________________________________________
> gmx-developers mailing list
> gmx-developers at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-developers
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-developers-request at gromacs.org.


-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++