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
>>>>
>>>>
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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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> AMBER.ambermd.org
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Received on Mon Jan 11 2021 - 06:30:05 PST
