[gmx-users] Energy conservation issue

[David van der Spoel]

On Thu, 2005-10-27 at 15:07 -0600, Yujie Wu wrote:
> Thanks, Berk.
> 
> <snipped>
> > 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
> whatsoever).
> 
> > 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.

> Yujie
> 
> 
> > 
> > Berk.
> > 
> 
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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://xray.bmc.uu.se/~spoel
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