Does the batch system create its own output file?
On 10/15/17 11:08 PM, Leena Aggarwal wrote:
> Yes, I am submitting job to batch system
>
> On Mon, Oct 16, 2017 at 11:37 AM, Leena Aggarwal <leena.hrc.gmail.com>
> 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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Received on Sun Oct 15 2017 - 23:30:03 PDT
