Dear David: Thanks a lot for your valuable help. Finally, I could reach my goal, i.e. apply simple sin-wave electric field. As you pointed out, the original GROMACS code already includes some time-dependent electric field function. However, for simple cos-wave (not the pulsed cos-wave), there is no phase term in the original code (up to 5.0.2). Then, it is not possible to change it sin-wave. Modify the line in mdlib/sim_util.c (function calc_f_el) as in the followings,
if (Et[m].n == 3) { t0 = Et[m].a[1]; Ext[m] = cos(Et[m].a[0]*(t-t0))*exp(-sqr(t-t0)/(2.0*sqr(Et[m].a[2]))); } else { /* Ext[m] = cos(Et[m].a[0]*t); original form */ Ext[m] = cos(Et[m].a[0]*(t-Et[m].phi[0])); /* modified form with phase */ } add the phase term for the simple cos-wave field. Then, mdp file lines in the followings, ; Electric fields ; Format is number of terms (int) and for all terms an amplitude (real) ; and a phase angle (real) E-x = 1 1.0 0.0 E-xt = 1 3.1415e-2 50.0 makes cos-wave electric fields with omega=3.1415e-2 (1/ps, period=200ps) and phase=50ps, i.e. sin-wave. Thanks a lot again. Makoto Yoneya, Dr. AIST, Tsukuba JAPAN > -----Original Message----- > From: Makoto Yoneya [mailto:makoto-yon...@aist.go.jp] > Sent: Thursday, October 02, 2014 5:08 PM > To: 'gmx-users' > Subject: source cord routines for electric fields > > Dear David: > > Thank a lot for your quick reply. > I'd found the code already includes some time-dependent function. > I'll study how to use it. > Thanks a lot again. > > Makoto Yoneya, Dr. > AIST, Tsukuba > JAPAN > > >On 2014-10-02 08:01, 米谷慎 wrote: > >> Dear Gromacs experts: > >> > >> I'd like to add the time-dependent function to the electric field > >> routines in GROMACS. > >> I could only found the input (reading) codes in src/kernel/readir.c. > >> Does anyone know which source cord routines I should modify to add > >> the time-dependent functions. > >> > >> Thank you for advance. > >> > >> Makoto Yoneya, Dr. > >> AIST, Tsukuba > >> JAPAN > >> > >mdlib/sim_util.c > >look for function calc_f_el > > > > > >-- > >David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. > >Biol., Uppsala University. > >Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.