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?
Mohammad
> On Jul 23, 2019, at 2:49 PM, David Cerutti <dscerutti.gmail.com> 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.
>
> DSC
>
>
> On Tue, Jul 23, 2019 at 2:10 PM Mohammad Hassan Khatami <
> MohammadHassan.Khatami.uoit.ca> 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
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Jul 23 2019 - 12:30:02 PDT
