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.*
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Received on Wed Feb 28 2024 - 01:30:02 PST
