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 - 07:00:02 PDT
