[gmx-developers] [Fwd: coulomb SR in 3.3cvs]
David
spoel at xray.bmc.uu.se
Mon Jul 18 19:32:41 CEST 2005
On Mon, 2005-07-18 at 17:31 +0200, Michel Cuendet wrote:
> Hi David,
>
> No, there is no LJ-LR when runnnig g_energy. (?)
>
> I'm using parrinello-rahman pressure coupling. But it seems to me that
> there is no significant difference related to that :
Is this from the same tpr? How can the density be different?
Did you check this:
http://www.gromacs.org/features/changes33.html
>
> 3.2.1 :
>
> ----------------------------------------------------------------
>
> Volume 887.289 1.27296 1.25576 -0.0555579 -0.722363
> pV -187.347 5068.08 5066.15 37.24 484.195
> Pressure (bar) -3.46691 94.8199 94.7838 0.697585 9.07
> Density (SI) 1005.13 1.44124 1.42162 0.0631539 0.821127
>
> 3.3
> ----------------------------------------------------------------
> Volume 887.104 1.40517 1.39327 0.0596162 0.632051
> pV 11.4915 5133.23 5129.17 66.7174 707.338
> Pressure (bar) 0.282085 96.0735 95.9974 1.24973 13.2496
> Density (SI) 1005.34 1.59044 1.57699 -0.0674518 -0.715124
>
>
> Thanks for your assitsance !
>
> Bye,
>
> Michel
>
> Below is my mdp file :
>
>
> constraints = hbonds
>
> integrator = md
>
> dt = 0.002 ; ps !
>
> nsteps = 2000000 ; total 4.0 ns.
>
> nstcomm = 1
>
> nstxout = 20000
>
> nstvout = 100000
>
> nstfout = 0
>
> nstlog = 1000
>
> nstenergy = 10
>
> nstxtcout = 10
>
> xtc_grps = System
>
> nstlist = 10
>
> ns_type = grid
>
> coulombtype = PME
>
> rlist = 1.0
>
> rcoulomb = 1.0
>
> vdwtype = shift
>
> rvdw_switch = 0.9
>
> rvdw = 1.0
>
> Tcoupl = nose-hoover
>
> tc-grps = Protein Other
>
> tau_t = 0.1 0.1
>
> ref_t = 300 300
>
> energygrps = T MHC_a12_Tax
>
> Pcoupl = parrinello-rahman
>
> Pcoupltype = isotropic
>
> tau_p = 1.0
>
> compressibility = 4.5e-5
>
> ref_p = 1.0
>
>
>
> David van der Spoel wrote:
>
> >On Mon, 18 Jul 2005, Michel Cuendet wrote:
> >
> >
> >
> >>Hi,
> >>
> >>I subitted this message already on the gmx-users mailing list, but got no
> >>feedback. I think it's an important issue for the CVS version 3.3. In the
> >>meantime, I could reproduce the problem on xeon cpus, so it's not itanium specific.
> >>
> >>
> >
> >Are these all the energies? No LJ-LR?
> >Are you running pressure coupling? If so check differences there as well.
> >
> >Do also check the revisions page.
> >
> >
> >
> >>Here is the original message :
> >>--------------------------------------------------------------------------------
> >>
> >>I compiled the 3.3 CVS version of 27.05.2005 on itanium2 with the intel
> >>8.1 compiler. (for those who don't know, the cvs version brings a
> >>terrific speedup on itaniums). Tests were performed with both versions
> >>in double precision.
> >>
> >>I compared the different energies obtained with 3.2.1 and 3.3, by taking
> >>the same trr (from a 3.2.1 equilibration, 85000 atoms, PME) and running
> >>it with both versions for about 12ps. From the tables below, one sees
> >>that there is a gap between Coulomb (SR) of 3450 KJ/mol, and between
> >>potential energies of 3280 KJ/mol.
> >>
> >>A close inspection of the energy files reveals that the version 3.3
> >>reproduces the same energy as 3.2.1 at the first step, but the system
> >>relaxes very quickly (0.5ps) to a lower energy with 3.3.
> >>
> >>Rerunning with 3.3 the trajectory produced by 3.2.1 surprisingly gives
> >>the correct energies.
> >>
> >>Any explaination for that ?
> >>
> >>Thanks,
> >>Michel
> >>
> >>
> >>3.2.1 :
> >>
> >>Energy Average RMSD Fluct. Drift Tot-Drift
> >>
> >>-------------------------------------------------------------------------------
> >>
> >>G96Bond 6723.8 140.873 138.612 -6.69756 -87.0817
> >>
> >>G96Angle 10213.6 173.746 173.579 2.02771 26.3642
> >>
> >>Proper Dih. 4446.16 89.4129 84.2042 8.01199 104.172
> >>
> >>Improper Dih. 3264.55 78.886 78.3318 -2.48685 -32.334
> >>
> >>LJ-14 852.608 79.621 79.52 1.0681 13.8874
> >>
> >>Coulomb-14 62903.9 126.041 122.079 -8.35397 -108.618
> >>
> >>LJ (SR) 166906 1099.22 1099.1 -4.19132 -54.4955
> >>
> >>Coulomb (SR) -1.2043e+06 1629.38 1629.34 -3.3074 -43.0028
> >>
> >>Coulomb (LR) -188686 91.952 90.6651 4.08445 53.106
> >>
> >>Potential -1.13768e+06 1031.78 1031.12 -9.84429 -127.995
> >>
> >>3.3 CVS
> >>
> >>Energy Average RMSD Fluct. Drift Tot-Drift
> >>
> >>-------------------------------------------------------------------------------
> >>
> >>G96Bond 6486.57 122.559 120.492 -7.32269 -77.6351
> >>
> >>G96Angle 10003.9 152.062 152.054 -0.496268 -5.26144
> >>
> >>Proper Dih. 4391.87 83.2508 80.8574 6.47554 68.6537
> >>
> >>Improper Dih. 3194.22 78.6896 78.6495 0.819815 8.69168
> >>
> >>LJ-14 833.553 76.0076 75.8776 -1.45206 -15.3947
> >>
> >>Coulomb-14 62899 124.539 123.82 -4.36711 -46.3001
> >>
> >>LJ (SR) 167720 1182.33 1157.55 78.6782 834.146
> >>
> >>Coulomb (SR) -1.20775e+06 1897.76 1850.85 -137.014 -1452.62
> >>
> >>Coul. recip. -188746 100.09 100.079 0.48938 5.18841
> >>
> >>Potential -1.14096e+06 1149.25 1132.33 -64.1897 -680.539
> >>
> >>
> >>
> >>
> >>
> >
> >
> >
>
--
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://xray.bmc.uu.se/~spoel
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