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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Received on Tue Oct 10 2017 - 23:30:03 PDT
