What does
$ file amyl_prod11.rst
give?
On 10/15/17 11:23 PM, Leena Aggarwal wrote:
> I have checked many times but I think it was not able to read the restart
> file in netcdf format
>
> On Mon, Oct 16, 2017 at 11:48 AM, Bill Ross <ross.cgl.ucsf.edu> wrote:
>
>> 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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>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> http://lists.ambermd.org/
>> mailman/listinfo/amber
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ______________________________
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>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> http://lists.ambermd.org/
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>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ______________________________
>> _________________
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> AMBER mailing list
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>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> http://lists.ambermd.org/
>> mailman/listinfo/amber
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Received on Sun Oct 15 2017 - 23:30:04 PDT
