Yes, I did one md step and got all non-zero forces. But for the energy minimization, all the forces are zero, althouth mdrun command gives non-zero forces.
On Sun, Jun 28, 2009 at 4:23 AM, Florian Dommert < [email protected]> wrote: > * 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> >>> <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 >> > > _______________________________________________ >> 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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