Re: AMBER: Regarding Dielectric Constant in AMBER8

From: <pande.vineet.fc.up.pt>
Date: Fri, 26 Nov 2004 16:45:47 +0000

.....Sorry..The complete input is:
ncyc and drms were "missing" in the last mail!
...


 &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,
                                                                ncyc = 500,
drms=0.01,
 &end
 &ewald
 eedmeth=5,
 &end
EOF


Quoting pande.vineet.fc.up.pt:

> 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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Received on Fri Nov 26 2004 - 16:53:00 PST
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