VMD-L Mailing List

From: Ropon-Palacios G. (groponp_at_gmail.com)
Date: Sat Sep 04 2021 - 22:05:10 CDT

Thank you very much Prof Fiorin for your explanation.

 

The only thing that worries me is that when I pulled with the SMD strategy in NAMD's config, when I was pulling for example the glycerol of chain A moved 1 Angstrom but the same could not happen for the other glycerol molecules in the other chains, and that made me unable to write a Tcl that obtains a coor, xsc with a windows of 1 Angstrom because the pulling was not symmetrical.

 

In this case, could pulling be semtric, using these colvar?

 

Finally, my question would be if it is necessary to specify the TargetStepNum or not?

 

Best,

 

Geo.

 

 

 

 

 

 

From: Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
Date: Saturday, September 4, 2021 at 7:51 PM
To: "Ropon-Palacios G." <groponp_at_gmail.com>
Cc: "Vermaas, Josh" <vermaasj_at_msu.edu>, VMD Mailing List <vmd-l_at_ks.uiuc.edu>
Subject: Re: vmd-l: Umbrella sampling windows

 

Hi Geo

 

On Sat, Sep 4, 2021 at 5:51 PM Ropon-Palacios G. <groponp_at_gmail.com> wrote:

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

 

No, but do take care of loading the Colvars state file when starting a new job (you don't need to if you issue multiple "run" commands within the same job). The step counter is saved in the Colvars state file, and the progress toward targetNumSteps is counted accordingly, e.g. you can have several jobs of 1M steps and targetNumSteps equal to 5M steps. In the second job, NAMD will report a step number of 0, but the Colvars traj file (and the internal state will continue from 1M steps and the restraint center will be set to where it's supposed to be).

 

For extracting frames over the SMD run, you can follow previous suggestions from the NAMD mailing list, or use the Dashboard with th latest alpha build of VMD:

https://urldefense.com/v3/__http://colvars.github.io/colvars-refman-vmd/colvars-refman-vmd.html*sec:dashboard__;Iw!!DZ3fjg!vam4pebsInLk6ezCa8H2CPe3Q0MzATGhGI1qHdT9xrX9RoAFrCJdDisMm33sBm5duA$

 

(This is the VMD mailing list, so after a lot of discussion about stuff that you do during a NAMD-simulation a VMD tip is in order).

 

Giacomo

 

 

 

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.