Adding to what Carlos said about the difficulty of treating explicit
ions in implicit water, when I mentioned pmemd supports few ions, I
meant that it strips the system of these ions before it calculates the
energy in GB for only the "solute+numwatkeep" water. It does not
calculate the GB energy with the ions in place.
On 3/11/20 1:32 PM, Carlos Simmerling wrote:
> well the hybrid solvent REMD method is a REMD variant that uses the hybrid
> solvent only in the exchange, in order to reduce the number of replicas
> that are needed. I'm not aware of and REMD simulation on an unfolded
> protein in explicit water than has been reported to work... and the hybrid
> method reduces the number of replicas, but also uses implicit
> solvent during the exchange and explicit salt that you desire has never
> been tested to my knowledge. You might be able to adapt it, but you would
> need to determine how to treat the explicit ions in the implicit water,
> which can be a real challenge. You would need to change the code as well.
> You might want to look into similar methods such as REST and see if they
> might be appropriate.
> I don't mean to dissuade you from the study, just to point out that your
> planned use has not been tested, and there are good reasons to think it
> will not work without some significant changes.
> carlos
>
> On Wed, Mar 11, 2020 at 1:14 PM Hosein Geraili Daronkola <
> geraili.hsn.gmail.com> wrote:
>
>> Carlos, why do you think it is not appropriate? What do you propose?
>> I just want enough sampling of the unfolded protein.
>>
>> Best
>>
>>
>>
>>
>> On Wed, Mar 11, 2020 at 4:39 PM Carlos Simmerling <
>> carlos.simmerling.gmail.com> wrote:
>>
>>> Unfortunately this method is not really appropriate for your needs, in my
>>> opinion.
>>>
>>> On Wed, Mar 11, 2020, 11:36 AM Hosein Geraili Daronkola <
>>> geraili.hsn.gmail.com> wrote:
>>>
>>>> Hi Koushik,
>>>>
>>>> Yes, I mean Replica Exchange MD simulation with a hybrid solvent
>> Exchange
>>>> scheme.
>>>>
>>>> The reason for using the explicit solvent is because I want to compare
>> it
>>>> with the native structure in the explicit solvent, and also the salt
>>>> concentration is very high (2 mol/kg).
>>>>
>>>> Thanks for the help
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> On Tue, Mar 10, 2020 at 9:24 PM koushik kasavajhala <
>>>> koushik.sbiiit.gmail.com> wrote:
>>>>
>>>>> 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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>>>>>>
>>>>> _______________________________________________
>>>>> AMBER mailing list
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>>>>>
>>>>
>>>> --
>>>> Hosein Geraili Daronkola
>>>> Ph.D. student,
>>>>
>>>> Wissenschaftspark Potsdam-Golm
>>>> Max Planck Institute of Colloids and Interfaces
>>>> Theory and Bio-Systems Department
>>>>
>>>> Office K-1.119
>>>> Am Mühlenberg 1 OT Golm
>>>> 14476 Potsdam
>>>> Germany
>>>>
>>>> Phone: +49-(0)331 567-9611
>>>> Fax: +49-(0)331 567-9602
>>>> E-mail: hosein.geraili.mpikg.mpg.de
>>>> _______________________________________________
>>>> AMBER mailing list
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>>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
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>>>
>>
>> --
>> Hosein Geraili Daronkola
>> Ph.D. student,
>>
>> Wissenschaftspark Potsdam-Golm
>> Max Planck Institute of Colloids and Interfaces
>> Theory and Bio-Systems Department
>>
>> Office K-1.119
>> Am Mühlenberg 1 OT Golm
>> 14476 Potsdam
>> Germany
>>
>> Phone: +49-(0)331 567-9611
>> Fax: +49-(0)331 567-9602
>> E-mail: hosein.geraili.mpikg.mpg.de
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
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Received on Wed Mar 11 2020 - 11:00:03 PDT
