I managed to install mdrun_d from CVS and the problem is fixed.... -----Original Message----- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Josiah Zayner Sent: Saturday, June 23, 2007 1:05 PM To: gmx-users@gromacs.org Subject: [gmx-users] Energy minimization problem with Double precision and mpi
Each time I try to run mdrun with double precision and more than one node, I always receive some atom with infinite Fmax, no matter what I do, Always on Step=0. The strangest thing is that it still attempts the minimization but the values never change except for Dmax in a steepest descent. If I change the coordinates of the atom that has the inf value another one has infinite value and so on. I use lam/mpi, with the command 'mpirun -np 5 mdrun_d -v -deffnm potd'. My double precision was configured with both --enable-mpi and --enable-double. Here is a copy of the mdp file I use: title = potd cpp = /usr/bin/cpp constraints = none integrator = steep nsteps = 0 ns_type = grid nstcomm = 1 nstlist = 10 rlist = 1.4 coulombtype = Shift vdw_type = Shift rcoulomb = 1.2 rvdw = 1.2 rcoulomb_switch = 1.0 rvdw_switch = 1.0 epsilon_r = 6.0 optimize_fft = yes emtol = 1000 emstep = 0.01 nstcgsteep = 100 It doesn't matter if it is in vaccum or water. I have minimized to an emtol of 10 and mdrun_d still does not work. I am using gromacs 3.3.1. I have tried changing or removing almost every value in the mdp file. I have tried different pdb files. Tried using grompp and grompp_d. Tried with -sort -shuffle and without. Is this another one of those compiler issues like genion? Any help would be great. Thanks, Josiah Zayner _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php