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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Received on Wed Oct 11 2017 - 11:00:02 PDT
