[gmx-users] intermolecular energy
Jones de Andrade
johannesrs at gmail.com
Sun Jun 24 06:18:07 CEST 2007
Ok, now here we go:
Energy Average RMSD Fluct. Drift
Tot-Drift
-------------------------------------------------------------------------------
Bond 2.06511 0.0619081 0 0.0891128
22.2784
Angle 2.62252 0.0641591 0 -0.0600975 -
15.0245
LJ (SR) -14.4123 0.0736452 0.0545518 0.000685531
0.171384
Disper. corr. -0.336488 0.00128091 0 0.000123901
0.0309754
Coulomb (SR) 0.132973 0.0164594 0 -0.00632308 -
1.58078
Coul. recip. -0.290073 0.0012684 0 0.000697912
0.174479
Potential -10.2183 0.128765 0 0.0241967
6.04921
Kinetic En. 7.67642 0.106321 0.105843 0.000139552
0.0348883
Total Energy -2.54186 0.163745 0 0.0243376
6.08444
Temperature 123.15 1.70567 1.70567 4.48689e-06
0.00112173
And that's working, using all Rlist, Rcoul and Rvdw as 1.3nm. Total energy
is the sum of potential and kinetic en., and potential is the sum of bond,
angle, lj(sr), disp.corr., coulomb(sr) and coul. recip.. Also, this means
that (obviously) the "U_inter" is equal to Potential minus bond minus angle,
or the sum of lj(sr), disp.corr., coulomb(sr) and coul. recip.
Just posted this last message with conclusions for record and in case it
become helpfull to someone else. Thanks a lot for everybody for the help in
all this subject!
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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