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 - 22:30:05 PDT
