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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> >>>>>>>>>>>>>>>>>>>>>>
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> >>>>>>>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>>>>>>>
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> >>>>>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>>>>>
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Received on Sun Oct 15 2017 - 23:00:04 PDT
