From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Sat Nov 15 2008 - 12:43:56 CST
what are the dimensions and center of your protein and your solvated
system prior to minimization? And how did you measure them?
Diego Alejandro Vargas wrote:
> 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 box.
> 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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