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 - 23:00:03 PDT
