* Shuangxing Dai <[email protected]> [2009-06-27 20:22:13 -0600]:
Yes, they are all zeros. I am confused why this happen. Thank you for help. And here is the mdp file:
That would confuse me, too. As I have never analyzed forces from a energy minimization, perhaps there is the problem. Try a zero-step md, meaning integrator=md and nsteps=0 and leave the further parameters unchanged. In case you get forces in your analysis then, we have discovered the source of error :) /Flo
; 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 < [email protected]> wrote:* Shuangxing Dai <[email protected]> [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" < [email protected]> To: "Discussion list for GROMACS users" <[email protected]> Sent: Saturday, June 27, 2009 3:20 PM Subject: Re: [gmx-users] force _______________________________________________gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php_______________________________________________ gmx-users mailing list [email protected] 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 [email protected]. 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: [email protected] 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 [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php-- Shuangxing Dai
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-- 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: [email protected] Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert !! PGP-ENCODED emails preferred !!
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