Ok, now here we go: Energy Average RMSD Fluct. Drift Tot-Drift ------------------------------------------------------------------------------- Bond 2.06511 0.0619081 0 0.0891128 22.2784 Angle 2.62252 0.0641591 0 -0.0600975 - 15.0245 LJ (SR) -14.4123 0.0736452 0.0545518 0.000685531 0.171384 Disper. corr. -0.336488 0.00128091 0 0.000123901 0.0309754 Coulomb (SR) 0.132973 0.0164594 0 -0.00632308 - 1.58078 Coul. recip. -0.290073 0.0012684 0 0.000697912 0.174479
Potential -10.2183 0.128765 0 0.0241967 6.04921 Kinetic En. 7.67642 0.106321 0.105843 0.000139552 0.0348883 Total Energy -2.54186 0.163745 0 0.0243376 6.08444 Temperature 123.15 1.70567 1.70567 4.48689e-06 0.00112173 And that's working, using all Rlist, Rcoul and Rvdw as 1.3nm. Total energy is the sum of potential and kinetic en., and potential is the sum of bond, angle, lj(sr), disp.corr., coulomb(sr) and coul. recip.. Also, this means that (obviously) the "U_inter" is equal to Potential minus bond minus angle, or the sum of lj(sr), disp.corr., coulomb(sr) and coul. recip. Just posted this last message with conclusions for record and in case it become helpfull to someone else. Thanks a lot for everybody for the help in all this subject! Sincerally yours, Jones On 6/23/07, David van der Spoel <[EMAIL PROTECTED]> wrote:
Jones de Andrade wrote: > Hi David. > > Well, as long as I can remember, I pushed the last gromacs sources at > time (3.3.1) and just installed it. Anyway, mdrun tells me it is 3.3 and > g_energy says it is 3.2.1 (in the run headers). I expected this to be > normal, or could I have run in some kind of unnexpected or unremembered > problem? > So that explains it: g_energy uses the names of the energy terms, and this exactly changed between 3.2 and 3.3. Hence Coul. Recip is not recognized as an energy term by the old g_energy. By the way you have rcoulomb > rlist, there you are using twin range cut-off. You probably want to make them identical. Now you are computing the energies for particles at distance between 1.25 and 1.30 only every nstlist steps, while you are computing the energies for particles at Rij <= 1.25 and particles at Rij>= 1.30 at every step. > About coul.recip.: Those results above, of the big list, all include > -nmol 500. It means that coul. recip. should be divided by 500² instead > of only 500? > > About twin-range: only if I'm unaware of it. In order to be sure, I'm > pasting here the mdp file I'm using. But, as far as I know, the answer > is no, I'm not using twin-range. > > Tnaks a lot in advance, > > Sincerally yours, > > Jones > > .mdp file follows: > > cpp = /lib/cpp > integrator = md > tinit = 3650.000 > dt = 0.002 > nsteps = 125000 > nstcomm = 1 > nstxout = 0 > nstvout = 0 > nstfout = 0 > nstxtcout = 10; 5 ;10 > xtc-precision = 1000 ;NAO MEXER! > nstlog = 10 > nstenergy = 10 > nstlist = 5 > energygrps = System > ns_type = grid > > ; Constraints use is: > constraints = none > constraint_algorithm = lincs > > ;Treatment of Vdw and Elctrostatics: > vdwtype = cut-off > DispCorr = EnerPres > rlist = 1.25 > rvdw = 1.25 > coulombtype = PME > rcoulomb = 1.30 > fourierspacing = 0.1 > pme_order = 4 > ewald_rtol = 1e-05 > optimize_fft = yes > > ; Temperature coupling is: > Tcoupl = nose-hoover > tau_t = 0.030 > tc-grps = System > ref_t = 123.15 > > ; Pressure coupling is: > Pcoupl = Parrinello-Rahman > pcoupltype = isotropic > tau_p = 2.500 > compressibility = 4.5e-5 > ref_p = 1.01325 ;bar == 1. atm > > ; Generate velocites at 123K is: > gen_vel = no > gen_temp = 123.15 > ;gen_seed = 173529 > gen_seed = 12041979 > > On 6/23/07, *David van der Spoel* <[EMAIL PROTECTED] > <mailto:[EMAIL PROTECTED]>> wrote: > > Jones de Andrade wrote: > > Hi all. > > > > First, I would like to apologize for the previous message. Maybe > I've > > been too "harsh"? Sorry for that. > > > > Second, I would like to list all the energetic contributions for one > > (same system, different run) run that g_energy allowed me to get: > > > > Energy Average RMSD Fluct. Drift > > Tot-Drift > > > ------------------------------------------------------------------------------- > > Bond 2.05116 0.0591887 0 - > 0.123751 > > -30.9381 > > Angle 2.638 0.0664036 0 0.114896 > > 28.7242 > > LJ (SR) -14.3726 0.0865671 0 - 0.0877988 > > -21.9499 > > Disper. corr. -0.378693 0.00211843 0 - 0.00185533 > > -0.463837 > > Coulomb (SR) 0.128875 0.0164563 0 0.000956545 > > 0.239138 > > Coulomb (LR) 0.00237452 4.3944e-05 0 3.95014e-05 > > 0.00987542 > > Coul. recip. - 145.145 0.660423 0.652976 > -0.00137031 > > -0.34258 > > Potential -10.2211 0.138681 0 - 0.0988822 > > -24.7207 > > Kinetic En. 7.67642 0.0990863 0.0988019 0.000103943 > > 0.025986 > > Total Energy -2.54473 0.167497 0 - 0.0987789 > > -24.6949 > > > > Temperature 123.15 1.5896 1.5896 3.34002e-06 > > 0.000835011 > > > Do you use an old version of g_energy with a newer mdrun? > > -- > David. > ________________________________________________________________________ > > David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, > Dept. of Cell and Molecular Biology, Uppsala University. > Husargatan 3, Box 596, 75124 Uppsala, Sweden > phone: 46 18 471 4205 fax: 46 18 511 755 > [EMAIL PROTECTED] > <mailto:[EMAIL PROTECTED]> [EMAIL PROTECTED] > <mailto:[EMAIL PROTECTED]> http://folding.bmc.uu.se > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > <mailto:gmx-users@gromacs.org> > http://www.gromacs.org/mailman/listinfo/gmx-users > <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] > <mailto:[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 -- David. ________________________________________________________________________ David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ _______________________________________________ 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
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