[gmx-users] reactive flux

Dear List, Does anyone have a script for running reactive flux calculations? I've put one together, but I'm not sure it's working properly, and I'd like to check it. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/list

[gmx-users] initial velocities

I am trying to integrate forward and backward in time from the same point. When I print out the initial velocities at <> time (either read in on the input file or generated with the same seed) they are not exactly the same for dt=-0.001 as for dt = +0.001 (as set in the mdp file). Is there a way

[gmx-users] problem with g_energy in 3.3.1

Users, I find that when I try to run the new g_energy, I don't get numbers by the categories (pressure, temperature, x-box, etc.) and can't select them. If I move the ener.edr file over to my other machine with 3.3, the thing reads fine. Anyone else have this problem in 3.3.1? Jim Rustad ___

[gmx-users] install problem

Dear GMX List, I am running into an installation problem with a recent version of the pathscale compiler when trying ./configure --enable-mpi I get "checking size of int... configure: error: cannot compute sizeof (int), 77" I searched the list and saw a similar problem with xlc, but no solutio

[gmx-users] graph edges bug?

Hi List, I am running into a "max graph edges exceeded" problem with gromacs 3.3. I can run my molecule fine with "pbc = no" but when I change it to "pbc = xyz" I get - Program mdrun_d, VERSION 3.3 Source code file: mshift.c, line: 95 Fa

[gmx-users] wham

Can anyone tell me how to use g_wham? The manual is a little cryptic about how tell wham what the relevant pdo files are. Thanks--Jim Rustad ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don'