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 - 23:00:05 PDT
