From: Alex Balaeff (abalaeff_at_polarisqb.com)
Date: Thu Sep 03 2020 - 11:31:51 CDT
Sounds awesome! -- best of luck :-)
On Thu, Sep 3, 2020 at 3:43 AM 辛志宏 <xzhfood_at_njau.edu.cn> wrote:
>
> 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
>
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>
> 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 Exitin
g: 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
>
>
-- ----- Dr. Alexander Balaeff Polaris Quantum Biotech www.PolarisQB.com (919)-270-5772
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