VMD-L Mailing List

From: Vermaas, Josh (vermaasj_at_msu.edu)
Date: Sat Sep 04 2021 - 16:10:37 CDT

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.