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
> > > >>>>>>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
> > > >>>>>>>>>>>>
> > > >>>>>>>>>>>>
> > > >>>>>>>>>>>>
> > > >>>>>>>>>>>> _______________________________________________
> > > >>>>>>>>>>>> AMBER mailing list
> > > >>>>>>>>>>>> AMBER.ambermd.org
> > > >>>>>>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
> > > >>>>>>>>>> _______________________________________________
> > > >>>>>>>>>> AMBER mailing list
> > > >>>>>>>>>> AMBER.ambermd.org
> > > >>>>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
> > > >>>>>>>>>>
> > > >>>>>>>>>>
> > > >>>>>>>>>>
> > > >>>>>>>>>> _______________________________________________
> > > >>>>>>>>>> AMBER mailing list
> > > >>>>>>>>>> AMBER.ambermd.org
> > > >>>>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
> > > >>>>>>>> _______________________________________________
> > > >>>>>>>> AMBER mailing list
> > > >>>>>>>> AMBER.ambermd.org
> > > >>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
> > > >>>>>>>>
> > > >>>>> _______________________________________________
> > > >>>>> AMBER mailing list
> > > >>>>> AMBER.ambermd.org
> > > >>>>> http://lists.ambermd.org/mailman/listinfo/amber
> > > >>>> _______________________________________________
> > > >>>> AMBER mailing list
> > > >>>> AMBER.ambermd.org
> > > >>>> http://lists.ambermd.org/mailman/listinfo/amber
> > > >>>>
> > > >>>>
> > > >>>>
> > > >>>> _______________________________________________
> > > >>>> AMBER mailing list
> > > >>>> AMBER.ambermd.org
> > > >>>> http://lists.ambermd.org/mailman/listinfo/amber
> > > >> _______________________________________________
> > > >> AMBER mailing list
> > > >> AMBER.ambermd.org
> > > >> http://lists.ambermd.org/mailman/listinfo/amber
> > > >>
> > > >>
> > > >>
> > > >> _______________________________________________
> > > >> AMBER mailing list
> > > >> AMBER.ambermd.org
> > > >> http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Oct 15 2017 - 22:00:02 PDT
