AMBER Archive (2004)Subject: Re: AMBER: Regarding Dielectric Constant in AMBER8
From: Carlos Simmerling (carlos_at_ilion.bio.sunysb.edu)
Date: Thu Nov 25 2004 - 10:45:34 CST
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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