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
> >>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
> >>>>>>>>>>>>>>>>>>>>>>>>>> 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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> >>>>>>>>>>>>>>>>>>>>>>>> AMBER mailing list
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> >>>>>>>>>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>>>>>>>>>
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Received on Sun Oct 15 2017 - 23:30:03 PDT
