[gmx-users] intermolecular energy
Jones de Andrade
johannesrs at gmail.com
Sun Jun 24 01:25:32 CEST 2007
Hi David.
Thanks a lot. Just trying it now.
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
Next linux installation I do it in a cleaner way. ;)
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.
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.
Thanks a lot!
Sincerally yours,
Jones
On 6/23/07, David van der Spoel <spoel at xray.bmc.uu.se> 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* <spoel at xray.bmc.uu.se
> > <mailto:spoel at xray.bmc.uu.se>> 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
> > spoel at xray.bmc.uu.se
> > <mailto:spoel at xray.bmc.uu.se> spoel at gromacs.org
> > <mailto:spoel at gromacs.org> http://folding.bmc.uu.se
> >
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> --
> 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
> spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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