VMD-L Mailing List

From: Catalin Buiu (cbuiu_at_yahoo.com)
Date: Wed Jun 26 2013 - 11:28:46 CDT

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 > > > > >