Re: Problems with minimization

From: Christopher Gillespie (
Date: Sat Nov 15 2008 - 12:10:46 CST


Problem 1: Box shrinking, maybe someone could correct me if I am wrong
but with minimization there should be no change in the box size since
no atoms have velocities meaning no temperature or pressure to correct
for. So as of right now I am not sure why the box appears to change
while the xsc file shows it does not.

Problem 2: Log file, the output from the minimization or any other
run will require you to use the following command line

charmrun namd2 +p7 /home/Diego/Diego/NAMD_2.6_Linux-amd64/
fascin_structures/wild_type/wt_2.conf > min.log

The output files you generated with the $outputfile variable are
exactly what it is supposed to create but the log file requires you to
add the " > filename.log " to the command line.

Hopefully that helps.

I would check on the "box" you display in VMD there may be something
incorrect about the way it is being displayed and not from the dcd file.


On Nov 15, 2008, at 12:53 PM, 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

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