[gmx-users] rerun problem
m.dalessandro at caspur.it
Wed Nov 5 13:44:01 CET 2003
the first problem was that the version of original results was 3.0.3 and in this
version the rerun didn't worked at all (giving shake error).
so I used the 3.1.4 version with which the rerun worked but giving bad results
in the calculation of LJ.
the only changes in the .mdp are :
1) constraints none in the rerun and h-bonds in the original
(this parameter was modified because otherwise the results of the rerun were
2) the temperature coupling was isothermal in the original and berendsen in the
rerun (because in the 3.1.4 release there is not the isothermal, but it
isn't a problem for me, since I don't need kinetic energy)
3) coulomb type PME for both.
about the results, I report you one frame of the original and rerun energy
LJ(14) Coulomb LJ(SR) Coulomb(SR)
original 1270.223417 18564.769168 59726.646291 -479536.291776
rerun 1269.997266 18562.972545 72114.672713 -479429.595416
As you can see the big problem is in the LJ(SR) rerun which is overestimated.
Do you think that the other quantities are in sufficient agreement or there is
some problem also in them?
e-mail : m.dalessandro at caspur.it
University of Rome "Tor Vergata"
Dep. of Chemical Science and Technology
Viale della Ricerca Scientifica, 00133 Roma
Quoting David van der Spoel <spoel at xray.bmc.uu.se>:
> On Wed, 2003-11-05 at 12:54, Maira d'Alessandro wrote:
> > hi!
> > I have just recalculated energy with the rerun option, but I have some
> > problems
> > with an overestimate of LJ (SR) values with respect to the original energy
> > calculation. the Coulombian energy works good but the LJ is about 15000 KJ
> > higher.
> > I used PME and shake for the simulation with 3.0.3
> > I tryed to make rerun with 3.0.3 but it didn't work.
> > Then I made the rerun with the 3.1.4 (without contraints) and it reproduced
> > all
> > the energy components except for the LJ.
> > can you give me some information about the way to obtain the correct LJ?
> Can you give more details about what is different between the original
> and the rerun?
> > --
> > Maira D'Alessandro
> > e-mail : m.dalessandro at caspur.it
> > Post-Doc researcher
> > University of Rome "Tor Vergata"
> > Dep. of Chemical Science and Technology
> > Viale della Ricerca Scientifica, 00133 Roma
> > tel 0039(0)672594905
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> David van der Spoel, PhD, Assist. 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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