[gmx-users] intermolecular energy
David van der Spoel
spoel at xray.bmc.uu.se
Sat Jun 23 22:25:08 CEST 2007
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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