From: Ashutosh Shandilya (scfbioiitd_at_gmail.com)
Date: Wed Nov 10 2021 - 13:26:59 CST
I also tried to increase harmonic restraints along the gz path from 0.5 to
5 but the problem still persists.
I switched off usesecondclosestframe off but it says
Error: keyword "usesecondclosestframe" is not supported, or not recognized
in this context
On Wed, Nov 10, 2021 at 2:23 PM Ashutosh Shandilya <scfbioiitd_at_gmail.com>
wrote:
> 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
> *)*
> 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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