From: Ashutosh Shandilya (scfbioiitd_at_gmail.com)
Date: Thu Nov 11 2021 - 10:15:37 CST
I am getting this type of warning
After running for 30000 steps it shows
TIMING: 30700 CPU: 579.654, 0.0178402/step Wall: 583.7, 0.0179331/step,
0.126628 hours remaining, 0.000000 MB of memory in use.
ENERGY: 30700 226234.5860 33319.1606 51301.2627 0.0000
-1814027.4858 224995.9113 0.0000 21.0432
376517.3497 -901638.1722 299.8428 -1278155.5219
-899427.3684 299.5875 1354.4689 44.7734
4458307.8773 0.5178 1.7157
*Warning: Geometrical pathCV relies on the assumption that the second
closest frame is the neighbouring frame*
*Please check your configuration or increase restraint on z (*This warning
comes earlier as well
*)*
I tried to increase *harmonic restraints* along the gz path from 0.5 to 5
but the problem still persists.
Frame index: 49 ; optimal RMSD = 0.975194
Frame index: 51 ; optimal RMSD = 0.975811
Frame index: 50 ; optimal RMSD = 0.977496
Frame index: 47 ; optimal RMSD = 0.994026
Frame index: 48 ; optimal RMSD = 0.995694
Frame index: 44 ; optimal RMSD = 1.00065
Frame index: 43 ; optimal RMSD = 1.00377
Frame index: 42 ; optimal RMSD = 1.00561
Frame index: 46 ; optimal RMSD = 1.00608
Frame index: 41 ; optimal RMSD = 1.0122
Frame index: 45 ; optimal RMSD = 1.01242
Frame index: 39 ; optimal RMSD = 1.02401
Frame index: 40 ; optimal RMSD = 1.02975
Frame index: 52 ; optimal RMSD = 1.03208
Frame index: 36 ; optimal RMSD = 1.03932
Frame index: 37 ; optimal RMSD = 1.04629
............
................
Frame index: 88 ; optimal RMSD = 3.32354
Frame index: 89 ; optimal RMSD = 3.75411
Frame index: 90 ; optimal RMSD = 3.7904
Frame index: 91 ; optimal RMSD = 3.80612
Frame index: 92 ; optimal RMSD = 3.8282
Frame index: 93 ; optimal RMSD = 3.83528
Frame index: 94 ; optimal RMSD = 3.84841
Frame index: 95 ; optimal RMSD = 3.86218
Frame index: 96 ; optimal RMSD = 3.89656
Frame index: 97 ; optimal RMSD = 3.97904
Frame index: 98 ; optimal RMSD = 4.16712
Frame index: 99 ; optimal RMSD = 4.18738
The error file gave following error
User defined signal 2
ERROR: One or more process (first noticed rank 8) terminated with signal 12
Kindly suggest,
Ashutosh
On Wed, Nov 10, 2021 at 12:11 PM Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
wrote:
> 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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