VMD-L Mailing List

From: Ryan McGreevy (ryanmcgreevy_at_ks.uiuc.edu)
Date: Wed Jun 26 2013 - 11:00:40 CDT

When you run mdff sim, you should see output in the VMD startup console
similar to:

Info) volmap: Computing bounding box coordinates
Info) volmap: grid minmax = {24 0 27} {77 65 65}
Info) volmap: grid size = 53x65x38 (0.5 MB)
Info) volmap: writing file "/usr/tmp/mdff_sim8268286412706732.dx".
MAP <- "/usr/tmp/mdff_sim8268286412706732.dx"
MAP :: gaussian blur (sigma = 2.5, regular)
MAP :: pad by x:9 9 y:9 9 z:9 9
MAP -> "test.dx"

Stats for MAP:
  WEIGHT: 1
  AVERAGE: 0.0565795
  STDEV: 0.15797
  MIN: 0
  MAX: 1.03341
  PMF_AVG: 0.0459067

If you are having the problem I suspect you are, you will not see any of
the lines beginning with "MAP". In the VMD console, could you please type
the following and let me know what happens:

*package require volutil*
*volutil*

On Tue, Jun 25, 2013 at 4:27 PM, Catalin Buiu <cbuiu_at_yahoo.com> wrote:

> Hello,
>
> When running the simple MDFF example (part 2 of the MDFF tutorial) I have
> the following problems. First, when generating a simulated density map
> (mdff sim command) no output was generated, even if intermediary .dx file
> were created. I had to generate the map in other program and import the
> result into VMD.
> Now I have problems with converting the density map to an MDFF potential.
> Again, there is no output for the mdff griddx command, i.e. no .dx file is
> generated.
> I would very much appreciate any help in this matter. I am running VMD on
> a Windows 8 machine.
>
> Thank you.
>
> Catalin Buiu
>
>
>
>
>