Read restrt in netcdf format. Also visualize the mdcrd file, to see if
anything went wrong.
On 10/15/17 9:38 PM, Leena Aggarwal wrote:
> After running the simulation, the restart file is now in binary cdf format.
> So, do we need to convert the restart file in ASCII format and then submit
> the further simulation. Or, do we need the changes in the production.in
> file so that it will read the restart file in netcdf format, i.e, ntx=6
> along with ntxo=0 and ioutfm=1
>
> On Fri, Oct 13, 2017 at 1:31 PM, Elvis Martis <elvis.martis.bcp.edu.in>
> wrote:
>
>> Fingers crossed
>>
>> Best Regards
>> Elvis Martis
>> Mumbai, INDIA.
>>
>> ________________________________________
>> From: Leena Aggarwal <leena.hrc.gmail.com>
>> Sent: 13 October 2017 11:19
>> To: AMBER Mailing List
>> Subject: Re: [AMBER] query regarding the restart file of molecular
>> dynamics simulation
>>
>> Right now, it is running. The restart file is in NetCDF format.
>>
>> On Thu, Oct 12, 2017 at 7:29 PM, Elvis Martis <elvis.martis.bcp.edu.in>
>> wrote:
>>
>>> DO you still get that error??
>>>
>>> Best Regards
>>> Elvis Martis
>>> Mumbai, INDIA.
>>>
>>> ________________________________________
>>> From: Leena Aggarwal <leena.hrc.gmail.com>
>>> Sent: 12 October 2017 17:42
>>> To: AMBER Mailing List
>>> Subject: Re: [AMBER] query regarding the restart file of molecular
>>> dynamics simulation
>>>
>>> Now, I am saving the restart files in netcdf format.
>>>
>>> On Thu, Oct 12, 2017 at 2:41 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
>>>
>>>> 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
>>>>
>>> _______________________________________________
>>> 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 Sun Oct 15 2017 - 22:00:02 PDT
