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 - 22:30:03 PDT
