Hi David.<br><br>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?
<br><br>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?<br><br>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.
<br><br>Tnaks a lot in advance,<br><br>Sincerally yours,<br><br>Jones<br><br>.mdp file follows:<br><br>cpp = /lib/cpp<br>integrator = md<br>tinit = 3650.000<br>dt =
0.002<br>nsteps = 125000<br>nstcomm = 1<br>nstxout = 0<br>nstvout = 0<br>nstfout = 0<br>nstxtcout = 10; 5 ;10<br>xtc-precision = 1000 ;NAO MEXER!
<br>nstlog = 10<br>nstenergy = 10<br>nstlist = 5<br>energygrps = System<br>ns_type = grid<br><br>; Constraints use is:<br>constraints = none<br>
constraint_algorithm = lincs<br><br>;Treatment of Vdw and Elctrostatics:<br>vdwtype = cut-off<br>DispCorr = EnerPres<br>rlist = 1.25<br>rvdw = 1.25<br>coulombtype = PME
<br>rcoulomb = 1.30<br>fourierspacing = 0.1<br>pme_order = 4<br>ewald_rtol = 1e-05<br>optimize_fft = yes<br><br>; Temperature coupling is:<br>Tcoupl = nose-hoover
<br>tau_t = 0.030<br>tc-grps = System<br>ref_t = 123.15<br><br>; Pressure coupling is:<br>Pcoupl = Parrinello-Rahman<br>pcoupltype = isotropic<br>tau_p =
2.500<br>compressibility = 4.5e-5<br>ref_p = 1.01325 ;bar == 1. atm<br><br>; Generate velocites at 123K is:<br>gen_vel = no<br>gen_temp = 123.15<br>;gen_seed = 173529
<br>gen_seed = 12041979<br><br><div><span class="gmail_quote">On 6/23/07, <b class="gmail_sendername">David van der Spoel</b> <<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>> wrote:</span>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Jones de Andrade wrote:<br>> Hi all.<br>><br>> First, I would like to apologize for the previous message. Maybe I've
<br>> been too "harsh"? Sorry for that.<br>><br>> Second, I would like to list all the energetic contributions for one<br>> (same system, different run) run that g_energy allowed me to get:<br>><br>
> Energy Average RMSD Fluct. Drift<br>> Tot-Drift<br>> -------------------------------------------------------------------------------<br>> Bond 2.05116
0.0591887 0 - 0.123751<br>> -30.9381<br>> Angle 2.638 0.0664036 0 0.114896<br>> 28.7242<br>> LJ (SR) -14.3726 0.0865671 0 -0.0877988
<br>> -21.9499<br>> Disper. corr. -0.378693 0.00211843 0 -0.00185533<br>> -0.463837<br>> Coulomb (SR) 0.128875 0.0164563 0 0.000956545<br>> 0.239138<br>> Coulomb (LR)
0.00237452 4.3944e-05 0 3.95014e-05<br>> 0.00987542<br>> Coul. recip. - 145.145 0.660423 0.652976 -0.00137031<br>> -0.34258<br>> Potential -10.2211 0.138681 0 -
0.0988822<br>> -24.7207<br>> Kinetic En. 7.67642 0.0990863 0.0988019 0.000103943<br>> 0.025986<br>> Total Energy -2.54473 0.167497 0 -0.0987789<br>> -24.6949<br>>
<br>> Temperature 123.15 1.5896 1.5896 3.34002e-06<br>> 0.000835011<br>><br>Do you use an old version of g_energy with a newer mdrun?<br><br>--<br>David.<br>________________________________________________________________________
<br>David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,<br>Dept. of Cell and Molecular Biology, Uppsala University.<br>Husargatan 3, Box 596, 75124 Uppsala, Sweden<br>phone: 46 18 471 4205 fax: 46 18 511 755
<br><a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a> <a href="mailto:spoel@gromacs.org">spoel@gromacs.org</a> <a href="http://folding.bmc.uu.se">http://folding.bmc.uu.se</a><br>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
<br>_______________________________________________<br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users
</a><br>Please search the archive at <a href="http://www.gromacs.org/search">http://www.gromacs.org/search</a> before posting!<br>Please don't post (un)subscribe requests to the list. Use the<br>www interface or send it to
<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</a><br></blockquote>
</div><br>