Hi Hosein,
Do you want to do a MD simulation with hybrid solvent or do you want to do
Replica Exchange MD simulation with a hybrid solvent Exchange scheme?
The point you mentioned pertains to Replica Exchange MD (REMD) using a
hybrid solvent exchange scheme. Hybrid solvent REMD using pmemd (to be
released with AMBER 20 version) allows systems with Na+, Cl-, and K+ ions
only. To my knowledge, hybrid Solvent REMD in sander does not support
systems with ions.
For a big system like yours, it may not be ideal to do explicit solvent
REMD. Is there a reason why you do not want to use GB with saltcon set to
some value?
Best,
Koushik
On Tue, Mar 10, 2020 at 4:09 PM Hosein Geraili Daronkola <
geraili.hsn.gmail.com> wrote:
> Hi all,
>
> I want to sample better my unfolded 129 residue protein in a high
> concentration of salt. The system is quite big, with 40000 water molecules.
> I want to use the hybrid solvent model for it, but what does this
> sentence mean?
>
> * 2. Explicit counterions should probably not be used.*
>
> in the *caution *section of the *Replica exchange using a hybrid solvent
> model *part of the 2018 manual.
>
> Best
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Received on Tue Mar 10 2020 - 13:30:02 PDT
