Have you plotted and assessed them? Any conclusions?
On 10/11/17 9:24 PM, Leena Aggarwal wrote:
> 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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Received on Wed Oct 11 2017 - 21:30:03 PDT
