VMD-L Mailing List

From: Ryan McGreevy (ryanmcgreevy_at_ks.uiuc.edu)
Date: Thu Jun 27 2013 - 12:41:52 CDT

So when you run mdff sim, there is *nothing* output to the console that
opens when you start VMD? Also, what version of VMD are you using?

On Wed, Jun 26, 2013 at 11:28 AM, Catalin Buiu <cbuiu_at_yahoo.com> wrote:

> Hello Ryan,
>
> I do not get any output in the console when I run mdff sim.
>
> This is what I get in what regards volutil:
>
> >Main< (1GC1) 25 % package require volutil
> 1.3
> >Main< (1GC1) 26 % volutil
> Warning) Temporary directory c: is not writable. Defaulting to current
> directory D:/mdff/1GC1
>
> I have also changed the temporary directory with set env(TMPDIR), but with
> no result: mdff sim and mdff griddx produce no results.
>
> Thanks, Catalin
>
>
> ------------------------------
> *From:* Ryan McGreevy <ryanmcgreevy_at_ks.uiuc.edu>
> *To:* Catalin Buiu <cbuiu_at_yahoo.com>
> *Cc:* "vmd-l_at_ks.uiuc.edu" <vmd-l_at_ks.uiuc.edu>
> *Sent:* Wednesday, June 26, 2013 7:00 PM
> *Subject:* Re: vmd-l: Problems with MDFF tutorial
>
> 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
>
>
>
>
>
>
>
>