Re: Keeping potassium ions out of an area during equilibration

From: Souvik Sinha (souvik.sinha893_at_gmail.com)
Date: Wed Jun 07 2017 - 01:37:38 CDT

Hi,

There I have a query regarding the description of the switching function.
Its written that at d = d0 , the function will have a value of n/m. But
looking at the function, it seems to be of an indeterminate form at d = d0.

Souvik

On Tue, Jun 6, 2017 at 10:29 PM, Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov>
wrote:

> Hi Charles,
>
> If you only care about keeping things out of the pore, but not really the
> direction, I'd actually use a coordnum collective variable. You can do the
> same sort of thing with the tcl forces interface, but there the scripting
> is a bit less straightforward, since instead of forcing the atom purely
> along z, technically you may want to force things towards the outside.
> Performancewise tclforces and collective variables are about equal if you
> choose sane reaction coordinates. If you use coordnum, this is what you'd
> do. First, you'd define the K ions as well as what you want to keep them
> away from:
>
> set allsel [atomselect top "all"]
> $allsel set beta 0
> set ksel [atomselect top "name K"]
> set psel [atosmleect top "noh and protein"]
> $ksel set beta 1
> $psel set beta 2
> $allsel writepdb tags.pdb
>
> Then you'd define a collective variable to drive the number of contacts
> between the ksel and psel groups to 0 (this goes in a seperate file.
> colvars.conf or something like that).
>
> colvar {
> name contacts
> upperWall 0
> upperWallConstant 1
> coordNum {
> group1 {
> atomsFile tags.pdb
> atomsCol B
> atomsColValue 1
> }
> group2 {
> atomsFile tags.pdb
> atomsCol B
> atomsColValue 2
> }
> #These last three parameters are up to you. See http://www.ks.uiuc.edu/
> Research/namd/2.12/ug/node57.html#SECTION0001341120000000000000 for more
> info.
> cutoff 6
> expNumer 8
> expDenom 16
> }
> }
>
> Then you'd add the required elements to your NAMD configuration file to
> use this new coordination number collective variable to eliminate contacts.
>
> colvars on
> colvarsConfig colvars.conf
>
> -Josh
>
> On 06/05/2017 10:04 PM, Charles Hoying wrote:
> Hi,
>
> I have a membrane protein that I want to equilibrate in NAMD without
> allowing K ions from the solvation/ionization to get close to it.
> Specifically, it has a pore with stable K+ binding sites on the outside, so
> during equilibration before I run simulations I want to keep K+ ions away
> from that pore.
>
> I was thinking of modifying the "keep_water_out.tcl" script from the NAMD
> Membrane Proteins Tutorial (http://www.ks.uiuc.edu/
> Research/namd/mailing_list/<https://na01.safelinks.
> protection.outlook.com/?url=http%3A%2F%2Fwww.ks.uiuc.edu%
> 2FResearch%2Fnamd%2Fmailing_list%2F&data=02%7C01%7CJoshua.
> Vermaas%40nrel.gov%7C9ba77d4822c64c8562ef08d4ac910c8a%
> 7Ca0f29d7e28cd4f5484427885aee7c080%7C1%7C0%7C636323186363244953&sdata=%
> 2FLcU9bjg8u0wJgqefq8JkC83M0brGYrZH15UIxa599E%3D&reserved=0>) to recognize
> and keep K+ ions out of the same region, but I don't know how.
> Specifically, I would like to keep the ions out of the dimensions: (-3 < x
> < 3), (-3 < y < 3), i.e. the pore axis.
>
> I am open to any and all suggestions whether the script or some other
> approach can help me solve the problem! Please let me know if there is
> anything I can clarify to help answer my question.
>
> Best,
> Charles
>
>
>

-- 
Souvik Sinha
Research Fellow
Bioinformatics Centre (SGD LAB)
Bose Institute
Contact: 033 25693275

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