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
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Received on Sun Jan 03 2021 - 13:30:03 PST
