VMD-L Mailing List

From: Ryan McGreevy (ryanmcgreevy_at_ks.uiuc.edu)
Date: Wed May 29 2013 - 14:32:53 CDT

Perhaps try running VMD as administrator if you can, I know I have had
issues with file permissions on Windows in the past, and perhaps VMD is
failing to write a file it needs. I can't seem to recreate your
specific issue, but am looking into what could be the cause.

Martin Jones wrote:
> I've also uninstalled VMD and reinstalled 1.9.1 and the mdff sim command behaves the same way.
>
> Any other ideas?
>
> Thanks,
> Martin
>
> -----Original Message-----
> From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] On Behalf Of Martin Jones
> Sent: Friday, May 24, 2013 3:29 PM
> To: vmd-l_at_ks.uiuc.edu
> Subject: RE: vmd-l: MDFF difficulties with mdff sim command
>
> The mdff sim command behaves the same, producing a dx file and then nothing else.
>
> The volutil command also behaves the same, after running "package require volutil".
>
> volutil xxx
>
> also just writes out a blank line.
>
> -----Original Message-----
> From: Ryan McGreevy [mailto:ryanmcgreevy_at_ks.uiuc.edu]
> Sent: Friday, May 24, 2013 3:10 PM
> To: Martin Jones
> Cc: vmd-l_at_ks.uiuc.edu
> Subject: Re: vmd-l: MDFF difficulties with mdff sim command
>
> After running:
>
> package require volutil
>
> try running the original mdff sim command again. The volutil plugin should have been loaded when you ran:
>
> package require mdff
>
> at the beginning of the tutorial, but perhaps for some reason it failed the first time.
>
> Martin Jones wrote:
>
>> I don't see any of the lines about MAP. If I type:
>>
>> volutil -o 4ake-target_autopsf.situs -pad -smooth 2.5
>> mdff_sim9472389537595394.dx
>>
>> Then nothing happens, except a blank line is written to the DOS Window.
>>
>> If I type
>>
>> volutil
>>
>> I get the same thing, a blank line.
>>
>> If I type
>>
>> package require volutil
>>
>> then it writes
>>
>> 1.3
>>
>> -----Original Message-----
>> From: Ryan McGreevy [mailto:ryanmcgreevy_at_ks.uiuc.edu]
>> Sent: Friday, May 24, 2013 2:37 PM
>> To: Martin Jones
>> Cc: vmd-l_at_ks.uiuc.edu
>> Subject: Re: vmd-l: MDFF difficulties with mdff sim command
>>
>> The DOS window should look like:
>>
>> Info) volmap: Computing bounding box coordinates
>> Info) volmap: grid minmax = {-23 -35 -39} {19 25 18}
>> Info) volmap: grid size = 42x60x57 (0.5 MB)
>> Info) volmap: writing file "C:/mdff_sim5400057963747558.dx".
>> MAP <- "C:/mdff_sim5400057963747558.dx"
>> MAP :: gaussian blur (sigma = 2.5, regular) MAP :: pad by x:9 9 y:9 9 z:9 9 MAP -> "4ake-target_autopsf.situs"
>>
>> Stats for MAP:
>> WEIGHT: 1
>> AVERAGE: 0.0439921
>> STDEV: 0.139313
>> MIN: 0
>> MAX: 1.00588
>> PMF_AVG: 0.0357282
>>
>> After that temporary .dx is written, the VMD plugin /volutil/ is run to blur it (e.g. volutil -o $filename -pad -smooth $sigma $tmpDX where $sigma is .5*$targetResolution and $tmpDX is the name of the temporary .dx). That .dx file should also be automatically deleted as well, but you can read it so for some reason your VMD is stopping after it makes the .dx file.
>>
>> Martin Jones wrote:
>>
>>
>>> The situs file is not there. Nothing is logged in the VMD DOS Window after volmap.
>>>
>>> What program is supposed to run next?
>>>
>>> -----Original Message-----
>>> From: Ryan McGreevy [mailto:ryanmcgreevy_at_ks.uiuc.edu]
>>> Sent: Friday, May 24, 2013 1:42 PM
>>> To: Martin Jones
>>> Cc: vmd-l_at_ks.uiuc.edu
>>> Subject: Re: vmd-l: MDFF difficulties with mdff sim command
>>>
>>> That .dx file is just a temporary file VMD creates before blurring it to the appropriate resolution and writing out the final file which is the 4ake-target_autopsf.situs. Check your current VMD working directory for the 4ake-target_autopsf.situs file.
>>>
>>> Martin Jones wrote:
>>>
>>>
>>>
>>>> Hello,
>>>>
>>>> I have started the MDFF tutorial, using VMD for WIN32 1.9.1 on
>>>> Windows
>>>> 7 (64 bit). The MDFF is version 0.2.
>>>>
>>>> When I issue the following command on page 9
>>>>
>>>> mdff sim $sel -res 5 -o 4ake-target_autopsf.situs
>>>>
>>>> Instead of a situs file, a dx file is created, e.g.
>>>>
>>>> mdff_sim5932482353380174.dx
>>>>
>>>> The first few lines of which is:
>>>>
>>>> # Data calculated by the VMD volmap function
>>>>
>>>> object 1 class gridpositions counts 43 61 57
>>>>
>>>> origin -22.5 -34.5 -38.5
>>>>
>>>> delta 1 0 0
>>>>
>>>> delta 0 1 0
>>>>
>>>> delta 0 0 1
>>>>
>>>> ...
>>>>
>>>> And the DOS window also reports (a different attempt is shown):
>>>>
>>>> Info) volmap: Computing bounding box coordinates
>>>>
>>>> Info) volmap: grid minmax = {-23 -35 -39} {20 26 18}
>>>>
>>>> Info) volmap: grid size = 43x61x57 (0.6 MB)
>>>>
>>>> Info) volmap: writing file "c:mdff_sim5816507840443639.dx".
>>>>
>>>> Any help would be appreciated!
>>>>
>>>> Thanks,
>>>>
>>>> Martin
>>>>
>>>> ______________________________
>>>>
>>>> _ _
>>>>
>>>> Martin K. Jones
>>>>
>>>> University of Alabama at Birmingham
>>>>
>>>>
>>>>
>>>>
>>>
>>>
>>>
>>
>>
>
>