-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 On 01/30/2011 01:18 PM, aldi asmadi wrote: > Dear all, > > I would like to know if there is a way in GROMACS to find or specify the > value of kappa (or Ewald coupling/splitting parameter) for the PME > technique that we use in our simulation. In my case, I would like to > perform simulations with a specified kappa value and a grid size of A x > A x A for the PME parameter. If I understand it correctly, the grid can > be specified by the following in GROMACS: fourier_nx = A, fourier_ny = > 6, and fourier_nz = A. For the kappa, I could not find any information > about it so far from the manual or our mailing list. > > Many thanks. > > Best regards, > Aldi >
Unfortunately, Gromacs does not allow to input the splitting parameter directly, however just a small change in src/gmxlib/ewald_util.c is necessary to interpret a negative ewald_rtol in the mdp file as the splitting parameter. Therefore add after the declaration of the variables in calc_ewaldcoeff (line 53): if (dtol<0.0){ return -dtol; } If you are furthermore interested in an estimate of the error introduced by your SPME parameters, try the tool g_pme_error, which also tells you in the output file the corresponding splitting parameter \beta for a certain cut-off and ewald_rtol. Together with g_tune_pme I have realized that a quite remarkable gain in performance can be achieved, if the tools are used hand in hand. /Flo - -- Florian Dommert Dipl.-Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart Phone: +49(0)711/685-6-3613 Fax: +49-(0)711/685-6-3658 EMail: domm...@icp.uni-stuttgart.de Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iEYEARECAAYFAk1FcXsACgkQLpNNBb9GiPn1nwCgnBPM16PsQuvKRLw4oThHLYG/ OYkAn0UZqPTHJORAU7hmulTNMFf+Z4tA =sx4Z -----END PGP SIGNATURE----- -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists