AMBER Archive (2000)

Subject: Question on DNA Simulation Using PME!

From: Dat H. Nguyen (nguyend_at_chem.ucdavis.edu)
Date: Wed Jul 12 2000 - 19:36:55 CDT

Hello:

I am running a simulation of a B-DNA system using PME under constant
pressure. After ~200ps of simulation, one strand of DNA suddently jumped
out of the box and a short time later, it will jump back in to the
simulation box. Is there anyway to turn off this kind of image
interactions? As I read the manual on the PME part, it said that PME is
not comparable with IFTRES=1 (page 153 of AMBER 5.0 Manual, Vol 1). But
when I set IFTRES = 0, the sander module printed out an error message
and quit. The error message said that it does not make sense to set
IFTRES to 0 while using PME. Can anyone provide me a suggestion for
fixing this problem? I need to measure a distance from one DNA strand to
another. So, I need to keep both starnds of DNA in the same box.

Thank you very much!

Dat