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 - 00:30:04 PDT
