No, I have not run the simulation with iwrap=1
On Wed, Oct 11, 2017 at 1:03 PM, Elvis Martis <elvis.martis.bcp.edu.in>
wrote:
> HI
> Did you run the simulations with "iwrap=1"?
>
> Best Regards
> Elvis Martis
> Mumbai, INDIA.
>
> ________________________________________
> From: Leena Aggarwal <leena.hrc.gmail.com>
> Sent: 11 October 2017 12:41
> To: AMBER Mailing List
> Subject: Re: [AMBER] query regarding the restart file of molecular
> dynamics simulation
>
> 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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> >>> >>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>> >>>>
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> >>> >>>>
> >>> >>>>
> >>> >>>>
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> >>> >>
> >>> >>
> >>> >>
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> >>
> >
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Received on Wed Oct 11 2017 - 01:30:02 PDT
