************** 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 - 00:30:03 PDT
