Using CHARMM-GUI membrane builder with NAMD

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
water molecules.

Best regards,
Ajasja

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