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?
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]> 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] [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
_______________________________________________ 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
