AMBER Archive (2004)

Subject: Re: AMBER: Regarding Dielectric Constant in AMBER8

From: Carlos Simmerling (carlos_at_ilion.bio.sunysb.edu)
Date: Fri Nov 26 2004 - 08:02:56 CST

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_at_stonybrook.edu
===================================================================

pande.vineet_at_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_at_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_at_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_at_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_at_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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>
>
>
>
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