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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Received on Wed Oct 11 2017 - 00:30:02 PDT
