Thanks Dac for your kind reply. I am using Amber16
and $AMBERHOME/dat/leap/parm/frcmod.ionsjc_spce file looks good but I do
not have any file $AMBERHOME/dat/rism1d/mdl/c_SPCE/Na+.mdl, rather there is
a folder $AMBERHOME/dat/rism1d/model which contains following files:
CIO.mdl Cl-.mdl DC4.mdl K+.mdl MG2.mdl Na+.mdl PL3.mdl Rb+.mdl
SPF.mdl TP3.mdl TP5.mdl
CL3.mdl Cs+.mdl IB.mdl Li+.mdl MOH.mdl NMA.mdl prepdat.pl SPC.mdl
T4E.mdl TP4.mdl
I do not have specific ion parameters for rism1d for different water
models. Do I have some installation problem ?
Thanks.
Rakesh Srivastava
Research Fellow
School of Computational & Integrative Sciences
Jawaharlal Nehru University, New Delhi-110067
India
On Fri, Jun 22, 2018 at 11:33 PM David A Case <david.case.rutgers.edu>
wrote:
> On Fri, Jun 22, 2018, Rakesh Srivastava wrote:
>
> >
> > Can anyone please tell me that why size and epsilon parameters for ions
> > (like Na+) in the frcmod
> > file and the mdl file (which is used in rism1d) are different. Actually,
> > the size difference is not only of a factor of 2^(1/6) and epsilon values
> > are quite different (though units in both are kcal/mol mentioned in
> manual).
>
> Could you be specific about exactly which files you are comparing?
>
> If I look for the Joung-Cheathm Na+ ions associated with SPCE water,
> here is what I find:
>
> 1. In $AMBERHOME/dat/rism1d/mdl/c_SPCE/Na+.mdl:
>
> %FLAG LJEPSILON
> %FORMAT(5e16.8)
> 3.52641800e-01
> %FLAG LJSIGMA
> %FORMAT(5e16.8)
> 1.21200000e+00
>
> 2. In $AMBERHOME/dat/leap/parm/frcmod.ionsjc_spce:
>
> Na+ 1.212 0.3526418
>
> These agree perfectly. If there are other pairs of files that seem to be
> in
> disagreement, please let us know.
>
> ...thx...dac
>
>
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Received on Fri Jun 22 2018 - 21:30:03 PDT
