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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Received on Sun Oct 15 2017 - 23:30:02 PDT
