Hi, Fabian
The pulling time and strength always depend on your system and choice of
reaction coordinates,
most time the steering should be completed within 1ns if the reaction
coordinate is good.
So you can try 500ns first, it should be fast if you are using GPU.
The strength is really hard to say, I would recommend 100kcal/mol first,
but sometimes for MULTI_RMSD,
it really needs large steering strength, so if you can not get the
steering well try to increase the strength
gradually.
Best
Feng
On Sun, Jan 3, 2021 at 4:09 PM Fabian Glaser <fabian.glaser.gmail.com>
wrote:
> Dear Feng,
>
> Thanks a lot this is very helpful!
>
> If so, once I get the correct path values, could you please suggest a
> skillful way to choose pulling strength and steering time?
>
> From the tutorials I saw a 10-100 pulling strength values and 10-50 ns
> pulling time, but would be grateful if you could give me some insight here
> too.
>
> Much obliged!
>
> Fabian
>
> Sent from my iPhone
>
> > On 3 Jan 2021, at 22:51, Feng Pan <fpan3.ncsu.edu> wrote:
> >
> > Hello, Fabian
> >
> > MULTI_RMSD is the weighted RMSD value of multiple groups of atoms, so you
> > if want to pull your system to
> > the reference coordinates, the path should be (x, 0), where x should be
> the
> > initial value of MULTI_RMSD of your structure,
> >
> > You can use formula get x value, but a much simpler way is just to set
> the
> > steering strength to zero and run a short time to finish,
> > since there is no actual steering, the monitor file will just output the
> > initial value.
> >
> > Best
> > Feng
> >
> >> On Sun, Jan 3, 2021 at 12:47 PM Fabian Glaser <fabian.glaser.gmail.com>
> >> wrote:
> >>
> >> Dear Experts,
> >>
> >> I would like to get some help about using the &smd + MULTI_RMSD flag. It
> >> seems to work fine but I just don’t find what exactly the meaning go the
> >> path variable, is it the start and and values of RMSD of all the atoms
> used
> >> in to define the MULTI_RMSD?
> >>
> >> I use path = 1, 0, since I thought those values are indeed the initial
> >> RMSD and the target final one (I would like a “perfect” superimposition)
> >> but I am not sure I am using the right values…
> >>
> >> Thanks!!
> >>
> >> Fabian
> >>
> >>
> >>
> >> Best,
> >>
> >> Fabian
> >>
> >> Fabian Glaser PhD
> >>
> >> Bioinformatics Knowledge Unit - BKU
> >> The Lorry I. Lokey Center for Life Sciences and Engineering
> >> Technion - Israel Institute of Technology, Haifa, Israel
> >> Web https://lokey.technion.ac.il/bioinformatic-knowledge-unit/
> >> Tel +972 (0) 4 8293701
> >>
> >>
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> >>
> >
> >
> > --
> > Feng Pan
> > PostDoc
> > Florida State University
> > Department of Statistics
> > Email: fpan3.ncsu.edu; fpan.fsu.edu
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
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>
--
Feng Pan
PostDoc
Florida State University
Department of Statistics
Email: fpan3.ncsu.edu; fpan.fsu.edu
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Received on Tue Jan 05 2021 - 07:00:02 PST
