VMD-L Mailing List

From: Catalin Buiu (cbuiu_at_yahoo.com)
Date: Thu Jun 27 2013 - 12:44:36 CDT

Yes, Ryan, there is no output at all.
The newest version.
Catalin

On 27.06.2013, at 20:41, Ryan McGreevy <ryanmcgreevy_at_ks.uiuc.edu> wrote:

> 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
>>
>>
>>
>>
>>
>>
>>
>