VMD-L Mailing List
From: JC Gumbart (gumbart_at_physics.gatech.edu)
Date: Tue Feb 20 2018 - 10:27:53 CST
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(Please copy the mailing list in your replies so others can benefit.)
Glad it worked! At some point, we’ll have to figure out what’s unusual about 2.12 for FFTK.
Best,
JC
> On Feb 20, 2018, at 11:16 AM, Gabi Heller <gthh3_at_cam.ac.uk> wrote:
>
> Yep! That seems to have solved it! Thank you!
>
> On 20 February 2018 at 15:43, JC Gumbart <gumbart_at_physics.gatech.edu <mailto:gumbart_at_physics.gatech.edu>> wrote:
> Can you try using NAMD 2.11? I vaguely recall seeing a weird issue once with NAMD 2.12 and FFTK. Please let us all know if it works.
>
> Best,
> JC
>
>> On Feb 20, 2018, at 9:09 AM, Gabi Heller <gthh3_at_cam.ac.uk <mailto:gthh3_at_cam.ac.uk>> wrote:
>>
>> Dear JC,
>>
>> Thanks for your reply. I am attaching the runscript and the debugging log. At the bottom of the debugging log it says "NAMD run complete" although it only ran for a second and the tutorial suggests that such a run should take a few minutes... Furthermore, the FFTK GUI still says "Status: Running" and it remains inactive. The output .log file was created but it is empty.
>>
>> Best,
>> Gabi
>>
>>
>> On 20 February 2018 at 07:20, JC Gumbart <gumbart_at_physics.gatech.edu <mailto:gumbart_at_physics.gatech.edu>> wrote:
>> It’s hard to suggest anything without any clue as to what’s happening. Use “write a runscript” first to share what you input. Then do “write a debugging log” and see if anything is output to that.
>>
>> Best,
>> JC
>>
>> > On Feb 16, 2018, at 7:05 AM, Gabi Heller <gthh3_at_cam.ac.uk <mailto:gthh3_at_cam.ac.uk>> wrote:
>> >
>> > Hi FFTK users,
>> >
>> > I seem to be having issues with Optimizing Bond and Angle Parameters (step 5.2) using FFTK. It seems that the program is running continuously for a very long time ("Status: Running.." on the GUI), without writing or updating any files after the initial ones have been created. I do not have any error messages.
>> >
>> > I am using vmd 1.9.4 with namd 2.12. To test whether the issue was with my fragment or the software itself I repeated step 5.2 of the ethanol tutorial (using the prepared input files), which also runs continuously for a very long time without seemingly doing anything...
>> >
>> > Is this normal? Do you have any suggestions?
>> >
>> > Thank you very much!
>> >
>> > All the best,
>> > Gabi
>> >
>>
>>
>> <baOpt_test.0.debug.log><BondedOpt-RunScript.tcl>
>
>
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