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
> > > > > _______________________________________________
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> > > > > AMBER.ambermd.org
> > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > >
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> > > > AMBER.ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > >
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> > >
> > >
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Received on Wed Jun 27 2018 - 06:30:02 PDT
