[gmx-users] Energy conservation issue
David van der Spoel
spoel at xray.bmc.uu.se
Fri Oct 28 08:52:36 CEST 2005
On Thu, 2005-10-27 at 15:07 -0600, Yujie Wu wrote:
> Thanks, Berk.
> > I would say that the LJ cut-off is the largest source of errors.
> > I don't know how DL_POLY handles this.
> I checked its code; it is a simple truncation (without smoothing
> > But setting
> > vdw-type = shift
> > rvdw = 0.85
> This gives an error saying it is shorter than rlist (=0.9), so I guess
> you meant rvdw-switch=0.85? -- I tried this. The energy conservation is
> a bit worse: drifting rate = 40 kJ/mol/ns vs previously 32 kJ/mol/ns.
> I would like to encourage you developers to double-check this to see if
> you can reproduce the energy drifting that I observed here.
I'm sorry but we don't have the resources to support this 3 year old
gromacs version, please upgrade to 3.3 and see whether the problem
persists. If so come back to the list.
> > should help a lot.
> > BTW Why are you using such an old Gromacs version?
> That is the only one currently working with PME on my linux box.
> > Berk.
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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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