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 - 22:30:02 PDT
