Re: [AMBER] Confined box for implicit solvent simulations

From: Mohammad Hassan Khatami <>
Date: Tue, 23 Jul 2019 19:23:27 +0000

Thanks David for your reply.
Just out of curiosity, if I have a small methane (or any other particle or ions) in an implicit water, will it diffuse until it reaches to the limitation of XYZ in pdb format?

> On Jul 23, 2019, at 2:49 PM, David Cerutti <> wrote:
> I don't think we handle implicit solvent and periodic boundary conditions
> at the same time. For a system that large, implicit solvent (the way we
> implement it) would be much slower than explicit solvent, anyway, and the
> consensus is that implicit solvent is not as accurate. A large speedup and
> sampling capability are needed to justify implicit solvent calculations,
> although there are cases where that is true. CHARMM has implemented
> implicit solvent membranes, but in those cases the membrane itself is a
> different dielectric regime, another form of implicit solvation amidst the
> implicit
> water.
> On Tue, Jul 23, 2019 at 2:10 PM Mohammad Hassan Khatami <
>> wrote:
>> Hi everyone!
>> I am trying to run simulations of lipid membrane in an implicit solvent.
>> However, I am unable to define a box for the implicit solvent simulations.
>> Is there anyway around it?
>> Best,
>> Mohammad
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Received on Tue Jul 23 2019 - 12:30:02 PDT
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