[MMTK] nMOLDYN Question

Salomon Turgman Cohen sturgman at gmail.com
Fri Mar 29 21:45:42 UTC 2013


I have converted a few trajectories from dl_poly to MMTK format via
nMOLDYN. After doing this, I realized that some of the molecule names in
the dl_poly trajectory had spaces in them. The problem is when I try to do
an analysis with nMOLDYN on these nc files. The object selection string
ends up something like this:

object objectname SPC WATER atomelement oxygen

I cannot get nMOLDYN to play nice with these. Is the only solution to
reconvert the trajectories without spaces in the objectnames? I have tried
to modify the object selection string like this:

object objectname "SPC WATER" atomelement oxygen
object objectname 'SPC WATER' atomelement oxygen
object objectname SPC\ WATER atomelement oxygen

for which nMOLDYN thinks the objectnames are "SPC, 'SPC, and SPC\\
respectively. Anyone know how to get around this?


Salomon Turgman Cohen
Postdoctoral Associate
Cornell University
(919) 341-9650
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