Re: AMBER: Regarding Dielectric Constant in AMBER8

From: <pande.vineet.fc.up.pt>
Date: Fri, 26 Nov 2004 16:35:43 +0000

Dear Prof. Simmerling:
Thanks a zilion for your help! I tried the following way in a progressive run; a
part of my script (for H minimization) is:

***
***
 &cntrl
 ntx = 1, ntrx = 1, ntpr = 10,
 ntb = 0,
 igb = 0,
 dielc = 4,
 cut = 12.0,
 scnb = 2.0, scee = 1.2,
 imin = 1, ntr = 1, restraint_wt=32, restraintmask=':* & !.H=', maxcyc = 2000,
 &end
 &ewald
 eedmeth=5,
 &end
***
***

The calculation runs beyond perfection, structure is quite reasonable :).... This
means that with eedmeth=5 in the ewald part and dielc = 4, in the upper section
we are actually implementing a distance-dependent dielctric 4r(i,j), right? One
another question.. In this non-periodic case of ewald sums, how shall i decide
for example on other PME flags like USE_PME (which I usually put 0 for PBCs to
save time..), and VDWMETH..? Shall they remain defaults, like I used in this
test?

Thanks again,
Kind Regards
Vineet



Quoting Carlos Simmerling <carlos.ilion.bio.sunysb.edu>:

> did you read the section of the manual that I suggested?
>
> this does what you are asking for, please just try it and carefully
> read the sander output to see what it is doing.
>
> ===================================================================
> Carlos L. Simmerling, Ph.D.
> Associate Professor Phone: (631) 632-1336
> Center for Structural Biology Fax: (631) 632-1555
> Stony Brook University Web: http://comp.chem.sunysb.edu/carlos
> Stony Brook, NY 11794-5115 E-mail: carlos.simmerling.stonybrook.edu
> ===================================================================
>
>
>
>
> pande.vineet.fc.up.pt wrote:
>
> >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 - 16:53:00 PST
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