VMD-L Mailing List

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Sat Sep 04 2021 - 19:50:44 CDT

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!oQZw9zmVaHrwz34k6w104b66sd85DVRwkvrCGlO0tkLRI9cg3SEGX-FUudm-JtVSvw$

(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.
>
>
>
>
>
>
>