I have checked many times but I think it was not able to read the restart
file in netcdf format
On Mon, Oct 16, 2017 at 11:48 AM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> Looking at how it ends:
>
> getting new box info from bottom of inpcrd
> | INFO: Old style inpcrd file read
>
> This indicates that a netcdf file was not detected. Check your run args
> to sander.
>
>
> On 10/15/17 11:15 PM, Leena Aggarwal wrote:
> > I have attached the output file.
> >
> > On Mon, Oct 16, 2017 at 11:39 AM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> >
> >> Are you submitting jobs to a batch system? How does the output file end?
> >>
> >>
> >> On 10/15/17 11:07 PM, Leena Aggarwal wrote:
> >>> Output file has been made but no error in the output file
> >>>
> >>> On Mon, Oct 16, 2017 at 11:18 AM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> >>>
> >>>> Are you submitting jobs to a batch system? If so, see if any output is
> >>>> being captured by it into some file.
> >>>>
> >>>>
> >>>> On 10/15/17 10:46 PM, Leena Aggarwal wrote:
> >>>>> It is not giving any error that why it s not running but it is not
> >>>> running
> >>>>> On Mon, Oct 16, 2017 at 11:08 AM, Bill Ross <ross.cgl.ucsf.edu>
> wrote:
> >>>>>
> >>>>>> Did you try searching google for the error msg?
> >>>>>>
> >>>>>>
> >>>>>> On 10/15/17 10:37 PM, Leena Aggarwal wrote:
> >>>>>>> yes
> >>>>>>>
> >>>>>>> On Mon, Oct 16, 2017 at 10:59 AM, Bill Ross <ross.cgl.ucsf.edu>
> >> wrote:
> >>>>>>>> Same error each way?
> >>>>>>>>
> >>>>>>>>
> >>>>>>>> On 10/15/17 10:26 PM, Leena Aggarwal wrote:
> >>>>>>>>> ntx=4 or 5 or 6, with all it is giving error.
> >>>>>>>>>
> >>>>>>>>> On Mon, Oct 16, 2017 at 10:42 AM, Bill Ross <ross.cgl.ucsf.edu>
> >>>> wrote:
> >>>>>>>>>> This is what the manual is telling me:
> >>>>>>>>>>
> >>>>>>>>>> ntx Option to read the initial coordinates, velocities and box
> >> size
> >>>>>> from
> >>>>>>>>>> the inpcrd file. Option 1 must be used when one is starting from
> >>>>>>>>>> minimized or model-built coordinates. If an MD restrt file is
> used
> >>>> as
> >>>>>>>>>> inpcrd, then option 5 is generally used (unless you explicitly
> >> wish
> >>>> to
> >>>>>>>>>> ignore the velocities that are present). = 1 (default)
> >> Coordinates,
> >>>>>> but
> >>>>>>>>>> no velocities, will be read; either formatted (ASCII) files or
> >>>> NetCDF
> >>>>>>>>>> files can be used, as the input file type will be auto-detected.
> >> = 5
> >>>>>>>>>> Coordinates and velocities will be read from either a NetCDF or
> a
> >>>>>>>>>> formatted (ASCII) coordinate file. Box information will be read
> if
> >>>>>> ntb >
> >>>>>>>>>> 0. The velocity information will only be used if irest = 1 (see
> >>>>>> below).
> >>>>>>>>>> On 10/15/17 10:06 PM, Leena Aggarwal wrote:
> >>>>>>>>>>> Can you suggest me how to read the restart file in netcdf
> format.
> >>>>>>>>>>> Do I need to change ntx=6
> >>>>>>>>>>> or do I need to change the file usage of sander i.e, -c or -y
> >>>>>>>>>>>
> >>>>>>>>>>> On Mon, Oct 16, 2017 at 10:11 AM, Bill Ross <ross.cgl.ucsf.edu
> >
> >>>>>> wrote:
> >>>>>>>>>>>> Read restrt in netcdf format. Also visualize the mdcrd file,
> to
> >>>> see
> >>>>>> if
> >>>>>>>>>>>> anything went wrong.
> >>>>>>>>>>>>
> >>>>>>>>>>>>
> >>>>>>>>>>>> On 10/15/17 9:38 PM, Leena Aggarwal wrote:
> >>>>>>>>>>>>> After running the simulation, the restart file is now in
> binary
> >>>> cdf
> >>>>>>>>>>>> format.
> >>>>>>>>>>>>> So, do we need to convert the restart file in ASCII format
> and
> >>>> then
> >>>>>>>>>>>> submit
> >>>>>>>>>>>>> the further simulation. Or, do we need the changes in the
> >>>>>>>>>> production.in
> >>>>>>>>>>>>> file so that it will read the restart file in netcdf format,
> >> i.e,
> >>>>>>>> ntx=6
> >>>>>>>>>>>>> along with ntxo=0 and ioutfm=1
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> On Fri, Oct 13, 2017 at 1:31 PM, Elvis Martis <
> >>>>>>>> elvis.martis.bcp.edu.in
> >>>>>>>>>>>>> wrote:
> >>>>>>>>>>>>>
> >>>>>>>>>>>>>> Fingers crossed
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>>> Best Regards
> >>>>>>>>>>>>>> Elvis Martis
> >>>>>>>>>>>>>> Mumbai, INDIA.
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>>> ________________________________________
> >>>>>>>>>>>>>> From: Leena Aggarwal <leena.hrc.gmail.com>
> >>>>>>>>>>>>>> Sent: 13 October 2017 11:19
> >>>>>>>>>>>>>> To: AMBER Mailing List
> >>>>>>>>>>>>>> Subject: Re: [AMBER] query regarding the restart file of
> >>>> molecular
> >>>>>>>>>>>>>> dynamics simulation
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>>> Right now, it is running. The restart file is in NetCDF
> >> format.
> >>>>>>>>>>>>>> On Thu, Oct 12, 2017 at 7:29 PM, Elvis Martis <
> >>>>>>>>>> elvis.martis.bcp.edu.in>
> >>>>>>>>>>>>>> wrote:
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>>>> DO you still get that error??
> >>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>> Best Regards
> >>>>>>>>>>>>>>> Elvis Martis
> >>>>>>>>>>>>>>> Mumbai, INDIA.
> >>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>> ________________________________________
> >>>>>>>>>>>>>>> From: Leena Aggarwal <leena.hrc.gmail.com>
> >>>>>>>>>>>>>>> Sent: 12 October 2017 17:42
> >>>>>>>>>>>>>>> To: AMBER Mailing List
> >>>>>>>>>>>>>>> Subject: Re: [AMBER] query regarding the restart file of
> >>>>>> molecular
> >>>>>>>>>>>>>>> dynamics simulation
> >>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>> Now, I am saving the restart files in netcdf format.
> >>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>> On Thu, Oct 12, 2017 at 2:41 PM, Bill Ross <
> >> ross.cgl.ucsf.edu>
> >>>>>>>>>> wrote:
> >>>>>>>>>>>>>>>> Were there any messages about vlimit being exceeded in
> >> mdout?
> >>>>>>>>>>>>>>>> If the numbers that overflow into *****'s are relatively
> >> few,
> >>>>>> you
> >>>>>>>>>>>> might
> >>>>>>>>>>>>>>>> be able to figure which atoms are the prime suspects, look
> >> at
> >>>>>> the
> >>>>>>>>>> last
> >>>>>>>>>>>>>>>> valid coordinates, and begin to speculate what went wrong.
> >>>>>>>> However,
> >>>>>>>>>> I
> >>>>>>>>>>>>>>>> would try saving to netcdf format to prevent overflow, and
> >>>>>>>> rerunning
> >>>>>>>>>>>>>>>> while saving to mdcrd frequently, then visualize the
> >>>> trajectory
> >>>>>> to
> >>>>>>>>>>>> more
> >>>>>>>>>>>>>>>> easily see where the problem starts.
> >>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>> On 10/12/17 2:00 AM, Leena Aggarwal wrote:
> >>>>>>>>>>>>>>>>> Yes, I have plotted and the energy, temperature have
> >>>>>> equilibrated
> >>>>>>>>>>>>>>>> properly.
> >>>>>>>>>>>>>>>>> On Thu, Oct 12, 2017 at 9:57 AM, Bill Ross <
> >>>> ross.cgl.ucsf.edu>
> >>>>>>>>>>>>>> wrote:
> >>>>>>>>>>>>>>>>>> Have you plotted and assessed them? Any conclusions?
> >>>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>>> On 10/11/17 9:24 PM, Leena Aggarwal wrote:
> >>>>>>>>>>>>>>>>>>> I am attaching the files of energy, temperature and
> >>>> pressure.
> >>>>>>>>>>>>>>>>>>> On Wed, Oct 11, 2017 at 11:01 PM, Bill Ross <
> >>>>>> ross.cgl.ucsf.edu
> >>>>>>>>>>>>>>> wrote:
> >>>>>>>>>>>>>>>>>>>> Have you plotted energy, temperature etc yet?
> >>>>>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>>>>> On 10/11/17 12:11 AM, Leena Aggarwal wrote:
> >>>>>>>>>>>>>>>>>>>>> There were no ************ at all in mdout , mdcrd
> and
> >>>>>> mdrst
> >>>>>>>>>>>>>>> before
> >>>>>>>>>>>>>>>>>> ~95
> >>>>>>>>>>>>>>>>>>>> ns.
> >>>>>>>>>>>>>>>>>>>>> ********* come in only the restart file after 95 ns.
> >>>>>>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>>>>>> On Wed, Oct 11, 2017 at 12:39 PM, Leena Aggarwal <
> >>>>>>>>>>>>>>>> leena.hrc.gmail.com>
> >>>>>>>>>>>>>>>>>>>>> wrote:
> >>>>>>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>>>>>>> ************** comes in the output coordinate file
> >> after
> >>>>>>>>>>>>>>> simulation
> >>>>>>>>>>>>>>>>>> run
> >>>>>>>>>>>>>>>>>>>> of
> >>>>>>>>>>>>>>>>>>>>>> ~95 ns
> >>>>>>>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>>>>>>> On Wed, Oct 11, 2017 at 12:33 PM, Leena Aggarwal <
> >>>>>>>>>>>>>>>> leena.hrc.gmail.com
> >>>>>>>>>>>>>>>>>>>>>> wrote:
> >>>>>>>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>>>>>>>> I have not plotted but there are no ************ in
> >> the
> >>>>>>>>>> output
> >>>>>>>>>>>>>>>>>>>> coordinate
> >>>>>>>>>>>>>>>>>>>>>>> file.
> >>>>>>>>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>>>>>>>> On Wed, Oct 11, 2017 at 11:35 AM, Bill Ross <
> >>>>>>>>>> ross.cgl.ucsf.edu
> >>>>>>>>>>>>>>>>>> wrote:
> >>>>>>>>>>>>>>>>>>>>>>>> Have you plotted temperature, pressure, energies
> and
> >>>> the
> >>>>>>>>>> like,
> >>>>>>>>>>>>>>> to
> >>>>>>>>>>>>>>>>>> see
> >>>>>>>>>>>>>>>>>>>>>>>> how well-equilibrated the system is?
> >>>>>>>>>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>>>>>>>>> Are there any *****'s in the .out files?
> >>>>>>>>>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>>>>>>>>> On 10/10/17 9:17 PM, Leena Aggarwal wrote:
> >>>>>>>>>>>>>>>>>>>>>>>>> I am attaching the input files of equilibration.
> >> The
> >>>>>>>> number
> >>>>>>>>>>>>>> of
> >>>>>>>>>>>>>>>>>> atoms
> >>>>>>>>>>>>>>>>>>>>>>>> in the
> >>>>>>>>>>>>>>>>>>>>>>>>> system is around 98055. I have done the heating
> >> from
> >>>> 0
> >>>>>> to
> >>>>>>>>>>>>>> 300K
> >>>>>>>>>>>>>>>> for
> >>>>>>>>>>>>>>>>>>>> 100
> >>>>>>>>>>>>>>>>>>>>>>>> ps
> >>>>>>>>>>>>>>>>>>>>>>>>> in NVT ensemble using Langevin thermostat. Then I
> >>>> have
> >>>>>>>>>>>>>>>> equilibrated
> >>>>>>>>>>>>>>>>>>>> the
> >>>>>>>>>>>>>>>>>>>>>>>>> system for 5 ns before production.
> >>>>>>>>>>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>>>>>>>>>> On Tue, Oct 10, 2017 at 8:35 PM, Bill Ross <
> >>>>>>>>>>>>>> ross.cgl.ucsf.edu>
> >>>>>>>>>>>>>>>>>>>> wrote:
> >>>>>>>>>>>>>>>>>>>>>>>>>> How long did you equilibrate before production?
> >> Best
> >>>>>> to
> >>>>>>>>>> send
> >>>>>>>>>>>>>>>> those
> >>>>>>>>>>>>>>>>>>>> .in
> >>>>>>>>>>>>>>>>>>>>>>>>>> files too.
> >>>>>>>>>>>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>>>>>>>>>>> Bill
> >>>>>>>>>>>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>>>>>>>>>>> On 10/10/17 6:47 AM, Leena Aggarwal wrote:
> >>>>>>>>>>>>>>>>>>>>>>>>>>> I am attaching the input protocol file or
> >>>> production
> >>>>>>>> run
> >>>>>>>>>>>>>>> input
> >>>>>>>>>>>>>>>>>>>> file.
> >>>>>>>>>>>>>>>>>>>>>>>>>>> On Tue, Oct 10, 2017 at 6:39 PM, Elvis Martis <
> >>>>>>>>>>>>>>>>>>>>>>>> elvis.martis.bcp.edu.in>
> >>>>>>>>>>>>>>>>>>>>>>>>>>> wrote:
> >>>>>>>>>>>>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>>>>>>>>>>>>> HI,
> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Can you also send you input protocol file?
> >>>>>>>>>>>>>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Best Regards
> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Elvis Martis
> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Mumbai, INDIA.
> >>>>>>>>>>>>>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>>>>>>>>>>>>> ________________________________________
> >>>>>>>>>>>>>>>>>>>>>>>>>>>> From: Leena Aggarwal <leena.hrc.gmail.com>
> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Sent: 10 October 2017 18:10
> >>>>>>>>>>>>>>>>>>>>>>>>>>>> To: amber.ambermd.org
> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Subject: [AMBER] query regarding the restart
> >> file
> >>>> of
> >>>>>>>>>>>>>>> molecular
> >>>>>>>>>>>>>>>>>>>>>>>> dynamics
> >>>>>>>>>>>>>>>>>>>>>>>>>>>> simulation
> >>>>>>>>>>>>>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>>>>>>>>>>>>> I am getting '********************' in the
> >> restart
> >>>>>>>> file.
> >>>>>>>>>>>>>> So,
> >>>>>>>>>>>>>>>>>> while
> >>>>>>>>>>>>>>>>>>>>>>>>>>>> resubmitting the simulation it is showing the
> >>>> error
> >>>>>> :
> >>>>>>>>>>>>>>> "getting
> >>>>>>>>>>>>>>>>>> new
> >>>>>>>>>>>>>>>>>>>>>>>> box
> >>>>>>>>>>>>>>>>>>>>>>>>>> info
> >>>>>>>>>>>>>>>>>>>>>>>>>>>> from bottom of inpcrd
> >>>>>>>>>>>>>>>>>>>>>>>>>>>> INFO : old style inpcrd file read".
> >>>>>>>>>>>>>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>>>>>>>>>>>>> "************" error in restart file.
> >>>>>>>>>>>>>>>>>>>>>>>>>>>> ************-392.8431438
> >>>>>> 141.4329232************-393.
> >>>>>>>>>>>>>>> 5314779
> >>>>>>>>>>>>>>>>>>>>>>>>>> 142.1394832
> >>>>>>>>>>>>>>>>>>>>>>>>>>>> ************-392.6209402 141.4041265
> 512.3461308
> >>>>>>>>>>>>>> -57.5257819
> >>>>>>>>>>>>>>>>>>>>>>>> 296.9723761
> >>>>>>>>>>>>>>>>>>>>>>>>>>>> 559.7273926-176.5667776*******
> *****
> >>>>>>>>>>>>>>>>>>>>>>>> 560.1020382-176.1418198*******
> >>>>>>>>>>>>>>>>>>>>>>>>>> *****
> >>>>>>>>>>>>>>>>>>>>>>>>>>>> 559.0035464-175.9871851*******
> *****
> >>>>>>>> 156.3070715
> >>>>>>>>>>>>>>>>>> 146.8340440
> >>>>>>>>>>>>>>>>>>>>>>>>>> 417.5014573
> >>>>>>>>>>>>>>>>>>>>>>>>>>>> 155.9575107
> >>>> 183.8644124-287.7859939*******
> >>>>>>>> *****
> >>>>>>>>>>>>>>>>>> 128.6822810
> >>>>>>>>>>>>>>>>>>>>>>>>>> -44.4453453
> >>>>>>>>>>>>>>>>>>>>>>>>>>>> ************ 127.7639674
> -44.0672594************
> >>>>>>>>>>>>>> 128.8132441
> >>>>>>>>>>>>>>>>>>>>>>>> -44.7128400
> >>>>>>>>>>>>>>>>>>>>>>>>>>>> ______________________________
> _________________
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> >>>>>>>>>>>>>>>>>>>>>>>>>>>> http://lists.ambermd.org/
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> >>>>>>>>>>>>>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>>>>>>>>>>>>> ______________________________
> _________________
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> >>>>>>>>>>>>>>>>>>>>>>>>>>>> http://lists.ambermd.org/
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> >>>>>>>>>>>>>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>>>>>>>>>>>>> ______________________________
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> >>>>>>>>>>>>>>>>>>>>>>>>>>>> http://lists.ambermd.org/
> mailman/listinfo/amber
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Received on Sun Oct 15 2017 - 23:30:04 PDT
