Re: [AMBER] query regarding the restart file of molecular dynamics simulation

From: Bill Ross <ross.cgl.ucsf.edu>
Date: Sun, 15 Oct 2017 23:18:32 -0700

Looking at how it ends:

 ¬†getting new box info from bottom of inpcrd
|  INFO: Old style inpcrd file read

This indicates that a netcdf file was not detected. Check your run args
to sander.


On 10/15/17 11:15 PM, Leena Aggarwal wrote:
> I have attached the output file.
>
> On Mon, Oct 16, 2017 at 11:39 AM, Bill Ross <ross.cgl.ucsf.edu> wrote:
>
>> Are you submitting jobs to a batch system? How does the output file end?
>>
>>
>> On 10/15/17 11:07 PM, Leena Aggarwal wrote:
>>> Output file has been made but no error in the output file
>>>
>>> On Mon, Oct 16, 2017 at 11:18 AM, Bill Ross <ross.cgl.ucsf.edu> wrote:
>>>
>>>> Are you submitting jobs to a batch system? If so, see if any output is
>>>> being captured by it into some file.
>>>>
>>>>
>>>> On 10/15/17 10:46 PM, Leena Aggarwal wrote:
>>>>> It is not giving any error that why it s not running but it is not
>>>> running
>>>>> On Mon, Oct 16, 2017 at 11:08 AM, Bill Ross <ross.cgl.ucsf.edu> wrote:
>>>>>
>>>>>> Did you try searching google for the error msg?
>>>>>>
>>>>>>
>>>>>> On 10/15/17 10:37 PM, Leena Aggarwal wrote:
>>>>>>> yes
>>>>>>>
>>>>>>> On Mon, Oct 16, 2017 at 10:59 AM, Bill Ross <ross.cgl.ucsf.edu>
>> wrote:
>>>>>>>> Same error each way?
>>>>>>>>
>>>>>>>>
>>>>>>>> On 10/15/17 10:26 PM, Leena Aggarwal wrote:
>>>>>>>>> ntx=4 or 5 or 6, with all it is giving error.
>>>>>>>>>
>>>>>>>>> On Mon, Oct 16, 2017 at 10:42 AM, Bill Ross <ross.cgl.ucsf.edu>
>>>> wrote:
>>>>>>>>>> This is what the manual is telling me:
>>>>>>>>>>
>>>>>>>>>> ntx Option to read the initial coordinates, velocities and box
>> size
>>>>>> from
>>>>>>>>>> the inpcrd file. Option 1 must be used when one is starting from
>>>>>>>>>> minimized or model-built coordinates. If an MD restrt file is used
>>>> as
>>>>>>>>>> inpcrd, then option 5 is generally used (unless you explicitly
>> wish
>>>> to
>>>>>>>>>> ignore the velocities that are present). = 1 (default)
>> Coordinates,
>>>>>> but
>>>>>>>>>> no velocities, will be read; either formatted (ASCII) files or
>>>> NetCDF
>>>>>>>>>> files can be used, as the input file type will be auto-detected.
>> = 5
>>>>>>>>>> Coordinates and velocities will be read from either a NetCDF or a
>>>>>>>>>> formatted (ASCII) coordinate file. Box information will be read if
>>>>>> ntb >
>>>>>>>>>> 0. The velocity information will only be used if irest = 1 (see
>>>>>> below).
>>>>>>>>>> On 10/15/17 10:06 PM, Leena Aggarwal wrote:
>>>>>>>>>>> Can you suggest me how to read the restart file in netcdf format.
>>>>>>>>>>> Do I need to change ntx=6
>>>>>>>>>>> or do I need to change the file usage of sander i.e, -c or -y
>>>>>>>>>>>
>>>>>>>>>>> On Mon, Oct 16, 2017 at 10:11 AM, Bill Ross <ross.cgl.ucsf.edu>
>>>>>> wrote:
>>>>>>>>>>>> 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
>>>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
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>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
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>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
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Received on Sun Oct 15 2017 - 23:30:04 PDT
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