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
> >>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
> >>>>>>>>>>>>>>>>>>>>>>>> AMBER mailing list
> >>>>>>>>>>>>>>>>>>>>>>>> AMBER.ambermd.org
> >>>>>>>>>>>>>>>>>>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>>>>>>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
> >>>>>>>>>>>>>>>>>>>>>>>> AMBER mailing list
> >>>>>>>>>>>>>>>>>>>>>>>> AMBER.ambermd.org
> >>>>>>>>>>>>>>>>>>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>>>>>>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
> >>>>>>>>>>>>>>>>>>>>>>>> AMBER mailing list
> >>>>>>>>>>>>>>>>>>>>>>>> AMBER.ambermd.org
> >>>>>>>>>>>>>>>>>>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>>>>>>>>>>>>>>>>>>> _______________________________________________
> >>>>>>>>>>>>>>>>>>>>>> AMBER mailing list
> >>>>>>>>>>>>>>>>>>>>>> AMBER.ambermd.org
> >>>>>>>>>>>>>>>>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>>>>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>>>>>>> _______________________________________________
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> >>>>>>>>>>>>>>>>>>>>
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Received on Sun Oct 15 2017 - 23:30:01 PDT
