Tutorial-l Mailing List

From: Jeronimo Terrones (jt451_at_cam.ac.uk)
Date: Wed Oct 11 2017 - 10:19:44 CDT

Hi!

I tried to do the "Simulation of Water Permeation Through Nanotubes"
tutorial but I'm unable to run the first simulation.

If I try to run the file "sim_short.conf" as-is it complains that
pairlistdist and/or cutoff are close to the size of PBCs and namd2
segfaults.

I noticed that the basis vectors are smaller than those suggested for
the VMD visualization so I modified these and reduced cutoff and
pairlistdist but I now get an "Atoms moving too fast; simulation has
become unstable" error.

Is anyone experiencing the same problem? Is there anything wrong with
the config file??

I also tried setting the start temperature to 300 instead of using the
Binvelocities, and allowing for a few relaxation steps, but I keep
getting the same error.

Any help will be very aoppreciated.

Regards,
Jeronimo

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