[gmx-users] bond deviates....
David van der Spoel
spoel at xray.bmc.uu.se
Tue Sep 17 17:21:58 CEST 2002
On Tue, 2002-09-17 at 16:56, MOLTENI at unisi.it wrote:
> shortly after the beginning of a MD simulation in DMSO I get some
> warnings like "pressure scaling more than 1%" and, after that, an error
> "bond deviates more than half its own length" (after which the
> simulation stops), and also the temperature seems to explode.
> Does anyone have an idea as to what can be the reason?
probably wrong density (too high) or not well minimized conformation
> Can it be due to the fact that I'm bringing the system directly from "0
> K" (energy minimization) to 300 K? Is it (more) advisable to do short MD
> runs at, let's say, 100 K --> 200 K and finally the "long" simulation at
> 300 K?
> A couple of other questions:
> - apart from the various changes in the topology file some of you
> already explained me about (thanks, by the way), is there anything else
> that has to be changed when doing MD in DMSO (instead of water)? For
> instance, what about the compressibility (of water) that is used by
> default? Should it be changed, and where?
Not so important as long as tau_p is reasonably large (>= 1 ps)
> - Is it really useful (and why) to do a short MD with position
> restraints on the protein, peptide.. before the "real" simulation?
> Also if I already energy minimized the system (protein + solvent)? I
> know there are no "universal recipes" on the scheme to follow (minimize
> first the protein in vacuo? minimize protein and solvent together? bring
> directly or stepwise to target temperature?...) but.... does any of you
> have one? ;-)
When the solvent is not equilibrated it may destabilize the protein
unnecessarily. Of course, this implies admitting that your protein
simulation will never reach true equilibrium.
> Thanks a lot in advance!
> Elena Molteni
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Dr. David van der Spoel, Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576, 75123 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://zorn.bmc.uu.se/~spoel
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