VMD-L Mailing List

From: Ropon-Palacios G. (groponp_at_gmail.com)
Date: Sat Sep 04 2021 - 16:24:03 CDT

Dear Josh,

 

Thank you very much for the help. I have few perhaps trivial questions.

 

in the colvar:

 

center is the initial position of each molecule and targetcenters would be the distance to which I want to take it, right?

 

in my case I want to go from 15 to -15, it would be: Center 15 and Targetcenter -15 right?

 

On the other hand does the targetNumStep have to be the same as the "run" in the namd config file?

 

Finally,

 

This could generate an easy trajectory for me, and then select, for example, all the molecular ones to an X windows without, for example, that one higher and others lower in the aquaporin channel?

 

 

Thank you.

 

Best,

 

Geo.

 

From: "Vermaas, Josh" <vermaasj_at_msu.edu>
Date: Saturday, September 4, 2021 at 4:10 PM
To: "Ropon-Palacios G." <groponp_at_gmail.com>, VMD Mailing List <vmd-l_at_ks.uiuc.edu>
Subject: Re: vmd-l: Umbrella sampling windows

 

Use colvars, define a colvar for each glycerol molecule, and treat them as their own SMD using colvars. Below is a colvars config file I use to move two molecules across a membrane. You can adapt this to 4 as needed.

 

-Josh

 

colvarsTrajFrequency 100

colvarsTrajAppend off

analysis off

 

colvar {

        name upper

        width 1.0

        distanceZ {

                main {

                        atomsFile system.pdb

                        atomsCol B

                        atomsColValue 1

                }

                ref {

                        atomsFile system.pdb

                        atomsCol B

                        atomsColValue -1

                }

        }

}

colvar {

        name lower

        width 1.0

        distanceZ {

                main {

                        atomsFile system.pdb

                        atomsCol B

                        atomsColValue 2

                }

                ref {

                        atomsFile system.pdb

                        atomsCol B

                        atomsColValue -1

                }

        }

}

 

harmonic {

        name harm

        colvars lower

        centers 0

        targetCenters -35

        forceConstant 5

        targetNumSteps 5000000

}

harmonic {

        name harm2

        colvars upper

        centers 35

        targetCenters 0

        forceConstant 5

        targetNumSteps 5000000

}

 

 

From: <owner-vmd-l_at_ks.uiuc.edu> on behalf of "Ropon-Palacios G." <groponp_at_gmail.com>
Date: Saturday, September 4, 2021 at 3:21 PM
To: VMD Mailing List <vmd-l_at_ks.uiuc.edu>
Subject: vmd-l: Umbrella sampling windows

 

Dear users,

 

I have a tetrameric model of an aquaporin with 4 glycerol molecules, which I have already balanced and now I want to generate the windows for the umbrella sampling, I first thought of using SMD to generate the windows, however when I pull not all of them They move in the same position (windows range 1 A), so I thought about moving them manually, but I don't know how to generate all the windows from the balance value, or how could I do it? So I can place the glycerol all in the same position (ie 15 14 13 12 .... 0) inside the aquaporine.

 

 

Thanks for your suggestions.

 

best,

 

Geo.