Were there any messages about vlimit being exceeded in mdout?
If the numbers that overflow into *****'s are relatively few, you might
be able to figure which atoms are the prime suspects, look at the last
valid coordinates, and begin to speculate what went wrong. However, I
would try saving to netcdf format to prevent overflow, and rerunning
while saving to mdcrd frequently, then visualize the trajectory to more
easily see where the problem starts.
On 10/12/17 2:00 AM, Leena Aggarwal wrote:
> Yes, I have plotted and the energy, temperature have equilibrated properly.
>
> On Thu, Oct 12, 2017 at 9:57 AM, Bill Ross <ross.cgl.ucsf.edu> wrote:
>
>> 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
>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>> AMBER mailing list
>>>>>>>>>>>> AMBER.ambermd.org
>>>>>>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>>>>>>>>
>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>> AMBER mailing list
>>>>>>>>>>>> AMBER.ambermd.org
>>>>>>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>> AMBER mailing list
>>>>>>>>>>>> AMBER.ambermd.org
>>>>>>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>>>>>> _______________________________________________
>>>>>>>>>> AMBER mailing list
>>>>>>>>>> AMBER.ambermd.org
>>>>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> _______________________________________________
>>>>>>>>>> AMBER mailing list
>>>>>>>>>> AMBER.ambermd.org
>>>>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>>>> _______________________________________________
>>>>>>>> AMBER mailing list
>>>>>>>> AMBER.ambermd.org
>>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>>>>
>>>>> _______________________________________________
>>>>> AMBER mailing list
>>>>> AMBER.ambermd.org
>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>> _______________________________________________
>>>> AMBER mailing list
>>>> AMBER.ambermd.org
>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> AMBER mailing list
>>>> AMBER.ambermd.org
>>>> http://lists.ambermd.org/mailman/listinfo/amber
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Oct 12 2017 - 02:30:03 PDT
