hexagonal crystal

From: Allison Langham (langham_at_dtc.umn.edu)
Date: Wed Mar 21 2007 - 11:22:26 CDT

I'm trying to run a simulation using a hexagonal crystal shape.
I have done the model building in CHARMM (using Roux's method for
building a bilayer) and now I want to use NAMD for the production
runs. However, after successfully building and minimizing the model in CHARMM, I try to load it into NAMD (after using
the crd2pdb conversion utility). In NAMD, the van der Waals energy is too
high (99999999.9999), probably due to bad image contacts, as using a much larger box definition in NAMD
results in a reasonable energy.

I know there is a trick to aligning an RHDO from charmm to namd to prevent
this, but is there any such trick for HEXA?



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