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
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Mar 01 2024 - 05:00:02 PST
