The first step is to decide why you need HREMD. If you don't have a
specific H change you want to use, then just constant pH should be your
plan.
On Fri, Mar 1, 2024, 11:14 AM Dulal Mondal <
babunmondal.chem.kgpian.iitkgp.ac.in> wrote:
> Thank you sir for reply.
> I can not understand which parameters I choose for running Hamiltonian
> remd. I want to generate 2d remd (constant ph and H remd). How can I
> Hamiltonian pointer?
>
> On Fri, 1 Mar, 2024, 7:05 pm Carlos Simmerling, <
> carlos.simmerling.gmail.com> wrote:
>
>> What is the hamiltonian change you want to use?
>>
>> On Fri, Mar 1, 2024, 8:18 AM Dulal Mondal <
>> babunmondal.chem.kgpian.iitkgp.ac.in> wrote:
>>
>>> Thank you sir for your reply. I run constant pH MD and constant pH REMD.
>>> But Now I am trying 2D REMD ( the combination of constant pH remd and
>>> Hamiltonian remd) to get free energy profile from protonated to
>>> deprotonated state or vice versa. (like Umbrella sampling).
>>>
>>> On Fri, Mar 1, 2024 at 6:13 PM Carlos Simmerling <
>>> carlos.simmerling.gmail.com> wrote:
>>>
>>>> I think that it would help if you can try to explain better what you
>>>> want to do. Do you want 2D remd? Do you have a hamiltonian that you want to
>>>> vary? Or is it just pH? Your previous emails left me uncertain about what
>>>> you are asking.
>>>>
>>>> On Fri, Mar 1, 2024, 2:08 AM Dulal Mondal via AMBER <amber.ambermd.org>
>>>> wrote:
>>>>
>>>>> Please any one response.
>>>>>
>>>>> On Wed, 28 Feb, 2024, 2:48 pm Dulal Mondal, <
>>>>> babunmondal.chem.kgpian.iitkgp.ac.in> wrote:
>>>>>
>>>>> > Dear Experts,
>>>>> > I also do not understand how to use the HAMILTONIAN pointer I use in
>>>>> the
>>>>> > mdin file.
>>>>> > The different replicas differ by a parameter inside their mdin
>>>>> files. I
>>>>> > also do not understand what the parameter corresponds to.
>>>>> >
>>>>> > On Wed, Feb 28, 2024 at 1:50 PM Dulal Mondal <
>>>>> > babunmondal.chem.kgpian.iitkgp.ac.in> wrote:
>>>>> >
>>>>> >> Dear Experts,
>>>>> >>
>>>>> >> I followed the tutorial http://jswails.wikidot.com/ph-remd
>>>>> constant ph
>>>>> >> remd. I create different replicas from pH 4.5 to 10.0 with 0.5 pH
>>>>> gap. But
>>>>> >> there is no hamiltonian part.
>>>>> >> On the other hand J Phys Chem B. 2012 Aug 2; 116(30):
>>>>> 10.1021/jp303385x.
>>>>> >> <
>>>>> https://www.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&retmode=ref&cmd=prlinks&id=22694266
>>>>> >,
>>>>> >> they do combination of constant ph and hamiltonian remd. Is it 2D
>>>>> remd?
>>>>> >>
>>>>> >> In the amber manual (amber 18) page no. 442.
>>>>> >> HAMILTONIAN
>>>>> >> Hamiltonian Replica Exchange with different mdins
>>>>> >> 0.0000
>>>>> >> 0.3333
>>>>> >> 0.6667
>>>>> >> 1.0000
>>>>> >> I do not understand the value it corresponds to.
>>>>> >> --
>>>>> >> *With regards,*
>>>>> >> *Dulal Mondal,*
>>>>> >> *Research Scholar,*
>>>>> >> *Department of Chemistry,*
>>>>> >> *IIT Kharagpur, Kharagpur 721302.*
>>>>> >>
>>>>> >
>>>>> >
>>>>> > --
>>>>> > *With regards,*
>>>>> > *Dulal Mondal,*
>>>>> > *Research Scholar,*
>>>>> > *Department of Chemistry,*
>>>>> > *IIT Kharagpur, Kharagpur 721302.*
>>>>> >
>>>>> _______________________________________________
>>>>> AMBER mailing list
>>>>> AMBER.ambermd.org
>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>
>>>>
>>>
>>> --
>>> *With regards,*
>>> *Dulal Mondal,*
>>> *Research Scholar,*
>>> *Department of Chemistry,*
>>> *IIT Kharagpur, Kharagpur 721302.*
>>>
>>
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Received on Fri Mar 01 2024 - 08:30:02 PST
