From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Fri Jul 30 2010 - 09:17:36 CDT
Dear NAMD users,
does anyone have any experiance using the files generated with CHARMM-GUI
membrane builder in NAMD? The xplor psf and the pdb files are of course not
a problem, but the input files for the equilibration (which consists of 6
steps) would need a lot of work to translate to NAMD configurations files.
Has anybody done this already?
For example I know there is the keep_water_out.tcl script (which has been
giving me problems during the kcsa tuturial, but I can't remember the
details now), but the same could be achieved using tcl boundary forces, or
the grid forces or perhaps simply by first fixing (or constraining) the
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