Re: Problems with minimization

From: Diego Alejandro Vargas (
Date: Sat Nov 15 2008 - 11:53:06 CST

Thank you for your quick reply. By collapsed I mean the box is smaller in
dimension. I solvated the protein such that the water would occupy 20
Angstrom in every direction from the outmost point of the protein: When I
look at the dcd file certain parts of the protein stick out of the water

My .xsc file is just one line: "48 0 0 0 58 0 0 0 46 62 89 10 0 0 0 0 0 0"
with the right cell basis vector values and cell origin.

The command line to run NAMD: "charmrun namd2 +p7
(I am using a linux cluster with Rock OS). I don't fully understand what you
mean by not redirecting the output: I thought I defined the output to be
found at:

outputName $outputname

I get the appropiated .coor and .vel restart files in the file I define
there I thought .log would be there as well.


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