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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Received on Thu Oct 12 2017 - 23:00:03 PDT
