[gmx-users] bond deviates....

MOLTENI at unisi.it MOLTENI at unisi.it
Tue Sep 17 16:56:47 CEST 2002


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? 

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?

- 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? ;-)

Thanks a lot in advance!

Elena Molteni

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