Hi, Fabian
The harm is used in &smd, which is the strength the steering harmonic
potential,
anchor_strength is used in $pmd, which is used to define the strength of
the restraint in umbrella sampling,
Here you should not just define anchor_position without defining
anchor_strength, and if you are running SMD,
defining harm and path is enough, you don't need to define anchor_position
and anchor_strength in the input file.
There are examples in the manual to show how to use those parameters.
Best
Feng
On Mon, Jan 11, 2021 at 9:20 AM Fabian Glaser <fabian.glaser.gmail.com>
wrote:
> Dear Feng,
>
> I would like to ask related questions if that is ok, this time I would
> like to use TORSION as my CV, actually multiple torsion angles. I came up
> with the example bellow as my input cv. But I am not sure I am doing it
> right. Is that the correct syntax for multi torsional values?
>
> What is the difference between the harm value and the anchor_strengh? Do I
> need to use both?
> Also, I guess also here the path starts with the query angles and ends
> with the target, which is the same that appears at the anchor position
> target, is that correct?
>
> Thanks!
>
>
> &colvar
>
> npath = 2
> nharm = 1
> harm = 50.0
> path = 0, -2
>
> cv_type = 'TORSION'
> cv_ni = 4,
> cv_i = 5, 7, 9, 15
> anchor_position = -3,-2.0,-2.0,3
> !anchor_strength = 100
> /
>
> &colvar
>
> npath = 2
> nharm = 1
> harm = 50.0
> path = 0.67, -1.8
>
> cv_type = 'TORSION'
> cv_ni = 4, cv_i = 7, 9, 15, 17
> anchor_position = -2,-1.8,-1.8,2
> !anchor_strength = 100
> /
>
>
>
>
> 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
>
> > On 5 Jan 2021, at 16:43, Feng Pan <fpan3.ncsu.edu> wrote:
> >
> > 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
> >>>>
> >>>>
> >>>> _______________________________________________
> >>>> AMBER mailing list
> >>>> AMBER.ambermd.org
> >>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>
> >>>
> >>>
> >>> --
> >>> 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
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> > --
> > 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
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Feng Pan
PostDoc
Florida State University
Department of Statistics
Email: fpan3.ncsu.edu; fpan.fsu.edu
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Received on Mon Jan 11 2021 - 12:30:03 PST
