Thats Ok..But I want to put "no BOX at ALL" and have solute under "vacuo
conditions", and treat electrostatics with a Distance-Dependent term (say
4r(i,j)..But to use EEDMETH flag of PME, we must specify all ewald conditions
as well, isnīt it ..like the dimensions of the box..etc.
Thats where my doubt is ..what Flag in AMBER8 replaces the IDIEL flag of earlier
versions?
Thanks
Vineet
Quoting Carlos Simmerling <carlos.ilion.bio.sunysb.edu>:
> in the AMBER manual, under "potential function":
>
>
> NTB Periodic boundary. If NTB .EQ. 0 then a boundary is NOT applied
> regardless
> of any boundary condition information in the topology file.
>
>
>
> pande.vineet.fc.up.pt wrote:
>
> >Thanks..
> >that message says:
> >
> >use 'dielc=xx' in the &cntrl namelist together with 'eedmeth=5' in the
> >&ewald namlist.
> >
> >But, I donīt want to evoke PME and PBCs, I would like to use Distance
> dependent
> >dielec. for non-periodic calculations, just like we could do in previous
> >versions by using IDIEL...
> >Regards,
> >Vineet
> >Quoting Carlos Simmerling <carlos.ilion.bio.sunysb.edu>:
> >
> >
> >
> >>the first and second results from a google search for
> >>"amber distance dependent dielectric"
> >>point to the answer in the amber archive:
> >>
> >>http://amber.ch.ic.ac.uk/archive/200404/0244.html
> >>
> >>pande.vineet.fc.up.pt wrote:
> >>
> >>
> >>
> >>>Dear AMBER Users:
> >>>
> >>>This question is about specifying the type of DIELECTRIC in Sander
> >>>
> >>>
> >>calculations.
> >>
> >>
> >>>When I use PBCs and PME, and specify dielc = 1.0, it refers to a constant
> >>>dielctric, which is reasonable in this case..
> >>>
> >>>BUT, if I want to perform a minimization with a DISTANCE DEPENDENT
> >>>
> >>>
> >>DIELCTRIC, in
> >>
> >>
> >>>AMBER8 what shall I do? Because IDIEL flag no longer works in AMBER8.. Is
> it
> >>>
> >>>
> >>that
> >>
> >>
> >>>if I specify dielc = 1.0, and do not use PBCs/PME, it would refer by
> default
> >>>
> >>>
> >>to
> >>
> >>
> >>>a "distance-dependent" and not a "constant"? And then how to switch on to
> >>>"constant" ,imagining that we are doing a stochastic simulation and we
> donīt
> >>>apply PBCs..
> >>>
> >>>Thanks in advance!
> >>>Vineet Pande
> >>>
> >>>
> >>>
> >>>
> >>>
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> >
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Received on Fri Nov 26 2004 - 08:53:00 PST
