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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> >>>>>>>>>>>>>>>>>> AMBER.ambermd.org
> >>>>>>>>>>>>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>>>>>>>>>>>>>>>
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Received on Sun Oct 15 2017 - 22:30:04 PDT
