Hi David.<br><br>Thanks a lot. Just trying it now.<br><br>The mistake of the g_energy was something I sould have expected: I use an old Suse version, which *has* gromacs 3.2 installed by standard. The paths where getting that one instyead of my actual one. I completelly forget that, specially cause for no reason the paths don't work, yast doesn't uninstall it and have to make use of the "alias" to get things working properly
<br><br>Next linux installation I do it in a cleaner way. ;)<br><br>About the twin range, I'm rerunning to correct it. I've really didn't notice that when I choose the simulatins parameters of this whole series a long time ago. Really thank you very much.
<br><br>I'll post again after I get the new results to let be in the list if it is correct now or still has something wrong. May help others.<br><br>Thanks a lot!<br><br>Sincerally yours,<br><br>Jones<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 David.<br>><br>> Well, as long as I can remember, I pushed the last gromacs sources at<br>> time (3.3.1) and just installed it. Anyway, mdrun tells me it is 3.3 and<br>> g_energy says it is
3.2.1 (in the run headers). I expected this to be<br>> normal, or could I have run in some kind of unnexpected or unremembered<br>> problem?<br>><br><br>So that explains it: g_energy uses the names of the energy terms, and
<br>this exactly changed between 3.2 and 3.3. Hence Coul. Recip is not<br>recognized as an energy term by the old g_energy. By the way you have<br>rcoulomb > rlist, there you are using twin range cut-off. You probably<br>
want to make them identical. Now you are computing the energies for<br>particles at distance between 1.25 and 1.30 only every nstlist steps,<br>while you are computing the energies for particles at Rij <= 1.25 and<br>particles at Rij>=
1.30 at every step.<br><br><br>> About coul.recip.: Those results above, of the big list, all include<br>> -nmol 500. It means that coul. recip. should be divided by 500² instead<br>> of only 500?<br>><br>> About twin-range: only if I'm unaware of it. In order to be sure, I'm
<br>> pasting here the mdp file I'm using. But, as far as I know, the answer<br>> 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>> On 6/23/07, *David van der Spoel* <
<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a><br>> <mailto:<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>>> wrote:<br>><br>> Jones de Andrade wrote:<br>> > Hi all.
<br>> ><br>> > First, I would like to apologize for the previous message. Maybe<br>> 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>> -------------------------------------------------------------------------------<br>> > Bond 2.05116 0.0591887 0 -<br>> 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<br>> -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>><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
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</a><br><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.
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