VMD-L Mailing List

From: Ropon-Palacios G. (groponp_at_gmail.com)
Date: Mon Aug 09 2021 - 10:58:46 CDT

Thanks so muchs Josh. 

--
Ropón-Palacios G. BSc., MSc. 
Computational biophysicist, 
Associate Research, 
Laboratorio de Modelagem Computacional, 
Departamento de Ciências Exatas, 
Universidad Federal de Alfenas, Minas Gerais, Brasil. 
Phone: +51 935 055240. 
E-mail: groponp_at_gmail.com. 
 
 
 
 
On 8/9/21, 8:00 AM, "Vermaas, Josh" <vermaasj_at_msu.edu> wrote:
    In my experience, getting the initial windows exactly right isn't a big
    deal. Normally, I make the simplifying assumption that my SMD tracks the
    reaction coordinate fairly well (which I can check! Always check this!),
    and then I can do something like the following:
    
    mol new system.psf
    mol addfile smd.dcd waitfor -1
    set minz -20 ; #Depends on your actual range!
    set maxz 20 ; #Depends on your actual range!
    set numreplicas [expr {$maxz - $minz + 1}]; #This assumes 1 Angstrom
    spacing.
    set asel [atomselect top "all"]
    for { set i 0 } { $i < $numreplicas } { incr i } {
        set frame [expr { int($i * [molinfo top get numframes] / $numreplicas)}]
        $asel frame $frame
        $asel writenamdbin replica-$i.coor
        pbc writexst replica-$i.xsc -first $frame -last $frame
    }
    
    On 8/9/21 12:31 AM, Ropon-Palacios G. wrote:
    > Dear users, 
    >
    > made an SMD to generate different windows on the Z + axis, how can I write the files to be able to carry out the simulations of independent windows every 1 Angstrom?
    >
    >  
    >
    > My biggest problem is how to select for example every 1 angstrom, I have calculated the displacement in Z as (Zi-Z0) throughout the pulling, but I don't know how to make a for that writes every 1 angstrom (xsc and coord ) files
    
    -- 
    Josh Vermaas
    Assistant Professor, MSU-DOE Plant Research Lab and Department of Biochemisty and Molecular Biology
    vermaasj_at_msu.edu
    https://urldefense.com/v3/__https://prl.natsci.msu.edu/people/faculty/josh-vermaas/__;!!DZ3fjg!sP5zNgv5m2lhPZWT50tiWvgALMV13ADYc7n7ktQt1wM6MtbLux-_8of7aXrCxshL_g$