From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Wed Nov 10 2021 - 11:10:42 CST
Hi Ashutosh, the "colvars" keyword is an ordinary NAMD configuration
keyword, not a Tcl command. It's a bit like "constraints" in this regard,
which would give you a similar error message if you added it late in the
NAMD script.
Just put "colvars on" early in the NAMD script before any run command, or
other commands that trigger the Tcl interpreter. You're not required to
add any Colvars configuration even with "colvars on".
Giacomo
On Wed, Nov 10, 2021 at 11:45 AM Ashutosh Shandilya <scfbioiitd_at_gmail.com>
wrote:
> Thanks for all your help. In the slurm output I am getting the following
> error which I am unable to understand. I have been trying several changes
> in input files to get the job running but still getting some errors. If you
> have some insight kindly suggest.
>
> FATAL ERROR: Setting parameter colvars from script failed!
>
> FATAL ERROR: Setting parameter colvars from script failed!
>
> The output file ends like this
> TCL: Running for 20 steps
> ENERGY: 6100 228438.5351 32958.7464 51721.4945
> 0.0000 -1882555.5410 258836.2061 0.0000 0.0000
> 374233.1041 -936367.4549 298.0237 -1310600.5589
> -934162.1854 295.8515 1073.5139 16.7110
> 4799315.6868 55.7822 1.3010
>
> WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 6100
> WRITING COORDINATES TO RESTART FILE AT STEP 6100
> FINISHED WRITING RESTART COORDINATES
> WRITING VELOCITIES TO RESTART FILE AT STEP 6100
> FINISHED WRITING RESTART VELOCITIES
> TCL: Setting parameter langevinTemp to 300
> REINITIALIZING VELOCITIES AT STEP 6100 TO 300 KELVIN.
> TCL: Running for 20 steps
> ENERGY: 6100 228438.5351 32958.7464 51721.4945
> 0.0000 -1882555.5410 258836.2061 0.0000 0.0000
> 377307.1621 -933293.3968 300.4717 -1310600.5589
> -931093.1616 300.4717 1103.2400 25.8758
> 4799315.6868 1103.2400 25.8758
>
> TCL: Setting parameter colvars to on
> FATAL ERROR: Setting parameter colvars from script failed!
>
>
> Many thanks,
> Ashutosh
>
> On Thu, Nov 4, 2021 at 11:43 PM Michael Robinson <
> michael.robinson1_at_monash.edu> wrote:
>
>> Hi Ashutosh,
>>
>> I suspect that won't be the first error in the log file - that's normally
>> something that happens after an initial error. If that's not the case, look
>> at the output of the supercomputer you were using to run it (something like
>> a SLURM output) to see if that caused it.
>>
>> Cheers,
>> Michael
>>
>> On Thu, 4 Nov. 2021, 2:38 am Ashutosh Shandilya, <scfbioiitd_at_gmail.com>
>> wrote:
>>
>>> I am running ABF with namd but it stopped abruptly after some thousand
>>> steps. The error file gave following error. I looked online but didn't find
>>> any conclusive answer.
>>>
>>> User defined signal 2
>>> ERROR: One or more process (first noticed rank 8) terminated with
>>> signal 12
>>>
>>> What could be the problem?
>>>
>>> Many thanks,
>>> Ashutosh
>>>
>>> On Thu, Oct 28, 2021 at 2:20 PM Ashutosh Shandilya <scfbioiitd_at_gmail.com>
>>> wrote:
>>>
>>>> Many thanks, it works now.
>>>>
>>>> Regards,
>>>> Ashutosh
>>>>
>>>> On Wed, Oct 27, 2021 at 8:28 PM Michael Robinson <
>>>> michael.robinson1_at_monash.edu> wrote:
>>>>
>>>>> Hi Ashutosh,
>>>>>
>>>>> Your input file has a line break between 'abf' and the curly bracket
>>>>> '{' that opens the configuration block - this is causing the ABF
>>>>> configuration block to be skipped, and so your input file is failing. I
>>>>> can't test your given file without the associated system, but I
>>>>> double-checked that this would occur with one of my own ABF input files,
>>>>> and this caused the same error.
>>>>>
>>>>> Hopefully that helps,
>>>>> Regards,
>>>>> Michael Robinson
>>>>>
>>>>> On Thu, 28 Oct 2021 at 06:56, Ashutosh Shandilya <scfbioiitd_at_gmail.com>
>>>>> wrote:
>>>>>
>>>>>> Hi All
>>>>>> I want to run eABF with namd and I am getting following errors
>>>>>>
>>>>>> colvars: Collective variables initialized, 2 in total.
>>>>>> colvars: Error: keyword "abf" found without configuration.
>>>>>> FATAL ERROR: Error in the collective variables module (see above for
>>>>>> details)
>>>>>> FATAL ERROR: Error in the collective variables module (see above for
>>>>>> details).
>>>>>>
>>>>>> I was able to run collective variables but when trying to run eABF it
>>>>>> gives an error. Kindly have a look at the attached input file and suggest.
>>>>>>
>>>>>> Many thanks
>>>>>>
>>>>>>
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