Thanks, Tyler for your kind reply. It was really helpful.
Rakesh Srivastava
Research Fellow
School of Computational & Integrative Sciences
Jawaharlal Nehru University, New Delhi-110067
India
On Wed, Jun 27, 2018 at 10:22 PM Tyler Luchko (Lists) <
tluchko.lists.gmail.com> wrote:
> ‘deprecated’ means that these keywords are still accepted but may not be
> in future versions of the software. All of these keywords have more
> descriptive replacements, which you can find in the manual.
>
> Tyler
>
> > On Jun 27, 2018, at 6:18 AM, Leena Aggarwal <leena.hrc.gmail.com> wrote:
> >
> > All the input parameters are explained in amber manual. For example,
> > nr- number of grid points that should be a product of small prime numbers
> > (36784=2^15 : Here taking too many grid points is not required. nr=16384
> is
> > more than enough although 36784 is also correct )
> > dr- grid spacing in real space
> > rout- Largest real space separation for output file which you have taken
> as
> > 384
> > kout=0 All grid points will be output in reciprocal space
> > Other ksave, progress and maxstep are related to the progress and output
> > printing of the iterations.
> > smear and abcor are related to electrostatics so we generally use the
> > default values.
> > Dielectric constant of water=78.497, temperature=298K and number of
> > species=3 i.e. Wat, Na+ and Cl- .
> > Density of water is almost correct and density of Na+ and Cl- you have
> > chosen according to your requirement.
> >
> >
> > On Wed, Jun 27, 2018 at 6:07 PM, Rakesh Srivastava <
> allahabad.21.gmail.com>
> > wrote:
> >
> >> Okay Leena, Thanks. But still, I doubt, if everything is correct then
> why
> >> there are warnings. Further, can you please tell me, how did you decide
> >> that everything is correct?
> >>
> >> Thanks.
> >>
> >> Rakesh Srivastava
> >> Research Fellow
> >> School of Computational & Integrative Sciences
> >> Jawaharlal Nehru University, New Delhi-110067
> >> India
> >>
> >>
> >>
> >> On Wed, Jun 27, 2018 at 6:00 PM Leena Aggarwal <leena.hrc.gmail.com>
> >> wrote:
> >>
> >>> Hi Rakesh
> >>>
> >>> These warnings come while reading the input parameters of the script. I
> >> do
> >>> not know the exact meaning of these warnings but irrespective of the
> >> script
> >>> these always come while running the rism1d script. I think these are
> just
> >>> the starting warnings which indicate that all the input parameters
> >>> mentioned in the script are read correctly.
> >>> Your script is running correctly.
> >>>
> >>> On Wed, Jun 27, 2018 at 3:54 PM, Rakesh Srivastava <
> >> allahabad.21.gmail.com
> >>>>
> >>> wrote:
> >>>
> >>>> Hello Leena, I am attaching the script.
> >>>> Thanks.
> >>>>
> >>>> Rakesh Srivastava
> >>>> Research Fellow
> >>>> School of Computational & Integrative Sciences
> >>>> Jawaharlal Nehru University, New Delhi-110067
> >>>> India
> >>>>
> >>>>
> >>>>
> >>>> On Wed, Jun 27, 2018 at 2:42 PM Leena Aggarwal <leena.hrc.gmail.com>
> >>>> wrote:
> >>>>
> >>>>> Can you send me TP3_NaCl.inp script.
> >>>>>
> >>>>> On Wed, Jun 27, 2018 at 11:04 AM, Rakesh Srivastava <
> >>>>> allahabad.21.gmail.com>
> >>>>> wrote:
> >>>>>
> >>>>>> Hello all, when I run the rism1d script for solvent preparation,
> >> the
> >>>> out
> >>>>>> file starts with following warnings. Can you please tell me what
> >>> these
> >>>>>> warnings mean.
> >>>>>>
> >>>>>> reading input data file: TP3_NaCl.inp
> >>>>>> WARNING> 'closur' is deprecated
> >>>>>> WARNING> 'outlst' is deprecated
> >>>>>> WARNING> 'routup' is deprecated
> >>>>>> WARNING> 'toutup' is deprecated
> >>>>>> WARNING> 'kshow' is deprecated
> >>>>>> WARNING> 'nis' is deprecated
> >>>>>> WARNING> 'maxste' is deprecated
> >>>>>> WARNING> 'delvv' is deprecated
> >>>>>> WARNING> 'tolvv' is deprecated
> >>>>>> WARNING> 'temper' is deprecated
> >>>>>>
> >>>>>> Thanks.
> >>>>>>
> >>>>>> Rakesh Srivastava
> >>>>>> Research Fellow
> >>>>>> School of Computational & Integrative Sciences
> >>>>>> Jawaharlal Nehru University, New Delhi-110067
> >>>>>> India
> >>>>>> _______________________________________________
> >>>>>> 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
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> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
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> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
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Received on Wed Jun 27 2018 - 22:30:04 PDT
