[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:
> Hi
> 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
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
Groeten, David.
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

More information about the gromacs.org_gmx-users mailing list