Re: Problems with minimization

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Sat Nov 15 2008 - 12:43:56 CST

Hi Diego,
what are the dimensions and center of your protein and your solvated
system prior to minimization? And how did you measure them?
Peter

Diego Alejandro Vargas wrote:
> Chris,
> 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
> /home/Diego/Diego/NAMD_2.6_Linux-amd64/fascin_structures/wild_type/wt_2.conf"
> (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.
>
> Diego
>

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:50:06 CST