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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> >>>>>>>>>>>>>>>>>>>>
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> >>>>>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>>>>>
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Received on Sun Oct 15 2017 - 23:00:02 PDT
