From: 辛志宏 (xzhfood_at_njau.edu.cn)
Date: Thu Sep 03 2020 - 02:41:43 CDT
Dear Alexander,Many thanks for your patient and help,
I reboot the computer and rebuild the Dir "mkdir /dev/shm/NAMD_Example1", and setup the QMSimsPerNode parameter as 10, now NAMD begin to running,
.............................................................
TCL: Minimizing for 100 steps
Info: List of ranks running QM simulations: 0, 1, 2, 3, 4, 5, 6, 7, 8, 9.
QMENERGY: 0 1.0000 -2167893.0965 -2166860.0414
Info: Writing QM charge output at step 0
Info: Writing QM position output at step 0
PRESSURE: 0 -69830.2 176278 191727 -60034.4 -52703.2 -96760.4 -95998.3 13116.5 -13732.4
GPRESSURE: 0 -104592 176841 191741 -59720.7 -87839.4 -97217.2 -95530.3 12889.8 -49075.6
ETITLE: TS BOND ANGLE DIHED IMPRP
..................................................................
In addition, I fix the issue "namd-l: Wrong number of basis-sets stored!" by the addition of the Elementcolumn using " prepare.qm.region.tcl" script (the example script in the Namd tutorial example).
Many thanks again.
Zhihong Xin
From: Alex Balaeff <abalaeff_at_polarisqb.com>
Date: 2020-09-03 11:08:03
To: "辛志宏" <xzhfood_at_njau.edu.cn>
Cc: namd-l <namd-l_at_ks.uiuc.edu>
Subject: Re: Re: namd-l: Re:Re: namd-l: Wrong number of basis-sets stored!>Yep, you are back to ORCA problems:
>
>[file orca_tools/Tool-GTO-Bases/basissets.cpp, line 706]: Wrong number
>of basis-sets stored!
>
>Something is wrong with your QM system that throws ORCA off balance.
>(So it crashes and doesn't create the QM forces file, hence the next
>NAMD error message.) Either with this specific system, or with the
>ORCA setup on your computer.
>
>To rule out the latter, try running test jobs with ORCA. If it works,
>next try running a simpler QMMM system, perhaps, a single QM water
>molecule in a box of MM water? If that works, look for the errors in
>setting up the ORCA input file in your protein system. Did the
>NAMD/ORCA interface set up all the ORCA input files correctly? (in
>that temporary ORCA directory, /dev/shm/...) Did it place the link
>atoms capping the broken QM-to-MM covalent bonds correctly? In which
>aspects do the ORCA input files generated by NAMD differ from the
>input files you used for your standalone ORCA tests? Etc.
>
>
>On Wed, Sep 2, 2020 at 10:25 PM 辛志宏 <xzhfood_at_njau.edu.cn> wrote:
>>
>>
>> Thank you Alexander,
>> I comment the "Continuing a job from the restart files", the isse was solved, a new error occoured,
>> .........................
>> Info: Optimizing 4 FFT steps. 1... 2... 3... 4... Done. Info: Startup phase 7 took 0.000311636 s, 195.152 MB of memory in use Info: Startup phase 8 took 3.5698e-05 s, 195.152 MB of memory in use Info: Startup phase 9 took 4.6682e-05 s, 195.152 MB of memory in use Info: Startup phase 10 took 3.589e-05 s, 195.152 MB of memory in use Info: Startup phase 11 took 3.5717e-05 s, 195.152 MB of memory in use LDB: Central LB being created... Info: Startup phase 12 took 8.3965e-05 s, 195.152 MB of memory in use Info: CREATING 574 COMPUTE OBJECTS Info: Startup phase 13 took 0.00159058 s, 196.34 MB of memory in use Info: Startup phase 14 took 5.0467e-05 s, 196.34 MB of memory in use Info: Startup phase 15 took 0.000121969 s, 199.719 MB of memory in use Info: Finished startup at 0.808486 s, 199.719 MB of memory in use TCL: Minimizing for 100 steps Info: List of ranks running QM simulations: 0. [file orca_tools/Tool-GTO-Bases/basissets.cpp, line 706]: Wrong number of basis-sets stored! ------------- Processor 0 Exiting: Called CmiAbort ------------ Reason: FATAL ERROR: Error reading QM forces file. FATAL ERROR: Error reading QM forces file.
>>
>>
>> Thank you for your kindly help.
>>
>> Zhihong XIn
>>
>>
>>
>> 发件人：Alex Balaeff <abalaeff_at_polarisqb.com>
>> 发送日期：2020-09-03 09:17:40
>> 收件人：namd-l <namd-l_at_ks.uiuc.edu>,"辛志宏" <xzhfood_at_njau.edu.cn>
>> 抄送人："Acharya, Atanu" <aacharya42_at_gatech.edu>
>> 主题：Re: namd-l: Re:Re: namd-l: Wrong number of basis-sets stored!>Zhihong:
>> >
>> >You should comment out the line
>> >
>> >Continuing a job from the restart files
>> >
>> >Like this:
>> >
>> >#Continuing a job from the restart files
>> >
>> >Best,
>> >
>> >Alexander.
>> >
>> >On Wed, Sep 2, 2020 at 8:33 PM 辛志宏 <xzhfood_at_njau.edu.cn> wrote:
>> >>
>> >> Dear Atanu,
>> >> Thank you for your help, please find the NAMD config and log file at the attachment.
>> >>
>> >> Zhihong Xin
>> >>
>> >>
>> >>
>> >>
>> >>
>> >> 发件人："Acharya, Atanu" <aacharya42_at_gatech.edu>
>> >> 发送日期：2020-09-03 02:45:48
>> >> 收件人："辛志宏" <xzhfood_at_njau.edu.cn>
>> >> 抄送人："namd-l_at_ks.uiuc.edu" <namd-l_at_ks.uiuc.edu>
>> >> 主题：Re: namd-l: Wrong number of basis-sets stored!
>> >>
>> >> Dear Zhihong,
>> >> Seems like there might be a typo in the input file.
>> >>
>> >> ERROR: The following variables were set in the
>> >> ERROR: configuration file but are NOT VALID
>> >> ERROR: Continuing
>> >> FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE
>> >>
>> >> Could you please share you config file?
>> >>
>> >> Atanu
>> >>
>> >> On Sep 2, 2020, at 10:48 AM, 辛志宏 <xzhfood_at_njau.edu.cn> wrote:
>> >>
>> >> Zhihong
>> >>
>> >>
>> >>
>> >
>> >
>> >--
>> > -----
>> > Dr. Alexander Balaeff
>> > Polaris Quantum Biotech
>> > www.PolarisQB.com
>> > (919)-270-5772
>>
>>
>
>
>--
> -----
> Dr. Alexander Balaeff
> Polaris Quantum Biotech
> www.PolarisQB.com
> (919)-270-5772
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