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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> >>>>>>>>
> >>>>>>>>
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Received on Wed Oct 11 2017 - 21:30:02 PDT
