From: Ropon-Palacios G. (
Date: Fri May 21 2021 - 20:25:10 CDT

Dear user,


I am simulating a membrane protein that has a long lateral displacement, which I have not been able to correct with pbctool, so I would like to do the simulation again, trying to be able to use a circular barrier of force to keep the protein in its center of mass with a freedom of move 5 Angstroms on the XY axis, without compromising its secondary structure or conformational changes. Could you please help me solve this with tcl?



I leave my script below.



   proc calcforces {} {

    global grp xc0 yc0 zc0

    global kforce

    global freq fout ofile


    loadcoords coords


    set rc $coords($grp)

    set xc [lindex $rc 0]

    set yc [lindex $rc 1]

    set zc [lindex $rc 2]


    set diffx [expr {$xc0 - $xc}]

    set diffy [expr {$yc0 - $yc}]

    #set diffz [expr {$zc0 - $zc}]

    set f {}

    set fx [expr {$kforce*$diffx}]

    set fy [expr {$kforce*$diffy}]

    #set fz [expr {$kforce*$diffz}]

    lappend f $fx $fy ; #$fz


    addforce $grp $f


    addenergy [expr {0.5*$kforce*$diffx*$diffx}]

    addenergy [expr {0.5*$kforce*$diffy*$diffy}]

    #addenergy [expr {0.5*$kforce*$diffz*$diffz}]


#    set currstep [getstep]

#    if {[expr {$currstep % $freq}] == 0} {

#    set fout [open $ofile a+]

#        puts $fout [format "%f %f %f %f" $currstep $xc $yc $zc]

#    close $fout

#    }





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