Yes, they are all zeros. I am confused why this happen. Thank you for help. And here is the mdp file: ; RUN CONTROL PARAMETERS = integrator = steep nsteps = 50 ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 1 nstvout = 1 nstfout = 1 ; Output frequency for energies to log file and energy file nstlog = 1 nstenergy = 1 ; Output frequency and precision for xtc file nstxtcout = 1 xtc-precision = 1000 ; ENERGY MINIMIZATION OPTIONS = ; Force tolerance and initial step-size = emtol = 1 emstep = 0.01 ; NEIGHBORSEARCHING PARAMETERS = ; nblist update frequency = nstlist =3 ; ns algorithm (simple or grid) = ns_type = simple ; Periodic boundary conditions: xyz or none = pbc = xyz ; nblist cut-off = rlist =0.9 ; OPTIONS FOR ELECTROSTATICS AND VDW = ; Method for doing electrostatics = coulombtype = Shift rcoulomb = 0.9 ; Dielectric constant (DC) for cut-off or DC of reaction field = epsilon-r = 1 ; Method for doing Van der Waals = vdw-type = Cut-off ; cut-off lengths = rvdw = 0.9 ; Spacing for the PME/PPPM FFT grid = fourierspacing = 0.1 ; FFT grid size, when a value is 0 fourierspacing will be used = fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ; EWALD/PME/PPPM parameters = pme_order = 6 ewald_rtol = 1e-05 epsilon_surface = 0 optimize_fft = no
And also another question, can Gromacs write out the energy for each atom at each step? Just like it did to the forces? I use this mdp file and only see the total energy for each step in the log file. Thanks again. On Sat, Jun 27, 2009 at 8:07 PM, Florian Dommert < domm...@icp.uni-stuttgart.de> wrote: > * Shuangxing Dai <shuangxing...@gmail.com> [2009-06-27 18:57:41 -0600]: > > The nstfout =1 in mdout.mdp. So this should not be where the problem is. >> > > So this was the most obvious mistake I could imagine and you see it is > always appreciated that you put your mdp file also to the list, that > everybody knows your input parameters. However in case you already told > gromacs to write out the data to the trr file it should be there. > So if you try: > > echo 0 | g_traj -f traj.trr -s topol.tpr -of > Only zeros are contained in force.xvg ?? > > /Flo > > > >> ----- Original Message ----- From: "Florian Dommert" < >> domm...@icp.uni-stuttgart.de> >> To: "Discussion list for GROMACS users" <gmx-users@gromacs.org> >> Sent: Saturday, June 27, 2009 3:20 PM >> Subject: Re: [gmx-users] force >> >> >> _______________________________________________ >>> 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/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/mailing_lists/users.php >>> >> >> _______________________________________________ >> 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/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/mailing_lists/users.php >> > > -- > Florian Dommert > Dipl.-Phys. > > Institute for Computational Physics > University Stuttgart > > Pfaffenwaldring 27 > 70569 Stuttgart > > Tel: +49 - 711 / 6856-3613 > Fax: +49 - 711 / 6856-3658 > > EMail: domm...@icp.uni-stuttgart.de > Home: > http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert<http://www.icp.uni-stuttgart.de/%7Eicp/Florian_Dommert> > > !! PGP-ENCODED emails preferred !! > > _______________________________________________ > 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/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/mailing_lists/users.php > -- Shuangxing Dai
_______________________________________________ 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/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/mailing_lists/users.php