Hello Rafael-- > > I'm trying to perform the structure determination of a peptide using > explicit solvent following the script in the examples of the program > to improve my results in a vacuum. But when I add the explicit > solvent and finished the simulation a lot of violations that aren't > in the vacuum simulation appeared. A lot of them are from terms of > the force field like bonds and dihedrals. > > Do you have any suggestions for this case? Is there a better explicit solvent > protocol to use in this case?
Violations in the DIHE term are usually not of concern, but you might look at your structures to make certain things look ok. Bond violations are more of a concern. Are there significantly more BOND violations than with the vacuum calculations? Is the corresponding energy large? best regards-- Charles ######################################################################## To unsubscribe from the XPLOR-NIH list, click the following link: http://list.nih.gov/cgi-bin/wa.exe?SUBED1=XPLOR-NIH&A=1
