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
Received on Thu Feb 29 2024 - 23:30:02 PST
