Re: [AMBER] query regarding the restart file of molecular dynamics simulation

From: Leena Aggarwal <leena.hrc.gmail.com>
Date: Mon, 16 Oct 2017 11:38:20 +0530

Yes, I am submitting job to batch system

On Mon, Oct 16, 2017 at 11:37 AM, Leena Aggarwal <leena.hrc.gmail.com>
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
>> >>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>> >>>>>>>>>>>>>>>>>>>>>>>> AMBER mailing list
>> >>>>>>>>>>>>>>>>>>>>>>>> AMBER.ambermd.org
>> >>>>>>>>>>>>>>>>>>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>> >>>>>>>>>>>>>>>>>>>>>>>>
>> >>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>> >>>>>>>>>>>>>>>>>>>>>>>> AMBER mailing list
>> >>>>>>>>>>>>>>>>>>>>>>>> AMBER.ambermd.org
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>> >>>>>>>>>>>>>>>>>>>>>>>>
>> >>>>>>>>>>>>>>>>>>>>>>>>
>> >>>>>>>>>>>>>>>>>>>>>>>>
>> >>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>> >>>>>>>>>>>>>>>>>>>>>>>> AMBER mailing list
>> >>>>>>>>>>>>>>>>>>>>>>>> AMBER.ambermd.org
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Received on Sun Oct 15 2017 - 23:30:02 PDT
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