From: Vlad Cojocaru (Vlad.Cojocaru_at_eml-r.villa-bosch.de)
Date: Mon Oct 29 2007 - 12:59:00 CDT
Dear Jerome,
Thanks a lot for answering ... I didnt realize that ABF can do what I
want ... I will study it a bit and get back to you if I have further
questions ...
Best
vlad
Jerome Henin wrote:
>Dear Vlad,
>The ABF code needs the same kind of vector routines that you are
>using. Our solution was to steal the file vectors.tcl from VMD, which
>implements some useful operations. It lives in the lib/abf directory
>of NAMD, you can source it into your script.
>As a side note, the "abscissa" variable for ABF has been modified
>since NAMD 2.6 and now works in a way similar to what you want to do,
>with two groups of atoms defining the direction. The difference is
>that ABF won't pull at constant velocity. In case you are interested
>anyway, the new file should be publicly available very soon.
>Best,
>Jerome
>
>On 10/29/07, Vlad Cojocaru <Vlad.Cojocaru_at_eml-r.villa-bosch.de> wrote:
>
>
>>Dear NAMD users,
>>
>>I would like to use Tcl forces to move an atom with constant velocity
>>along a directon defined by two other atoms in the protein (an internal
>>direction which would change between time steps in function of how the
>>protein translates and/or rotates). Below I attach an attempt of script
>>to do that. However, I am not sure whether this is a correct script and
>>NAMD complains about the "vecnorm" command.
>>
>>First I would like to ask whether somebody has performed such a task in
>>NAMD and if the script below seems reasonablefor this? If yes, could
>>somebody indicate me how to calculate the direction in each time step
>>without using "vecnorm" (using only routines implemented in namd)?
>>
>>Thanks in advance
>>Best wishes
>>vlad
>>
>>----tcl script ---------
>>
>>set id1 7614
>>set id2 1193
>>set id3 3101
>>
>>set atoms {}
>>lappend atoms $id1 $id2 $id3
>>foreach atom $atoms {
>> addatom $atom
>>}
>># set the SMD output frequency, initialize the time counter,
>>set Tclfreq 50
>>set t 0
>>#set force constant in kcal/mol AA^2 and pulling vel. in AA/ts;
>>set k 7.2
>>#set velocity to be 35 A/100 ps
>>set v 0.00035
>>
>># initial coordinates of pulled atom (t = 0)
>>set x0 52.842
>>set y0 50.161
>>set z0 51.822
>>
>>set outfilename smd_tcl.out
>>open $outfilename w
>>
>>proc calcforces {} {
>>
>> global atoms id1 id2 id3 Tclfreq t k v x0 y0 z0 outfilename
>>
>> # form local array coords
>>
>> loadcoords coords
>>
>># calculate direction of pulling
>>
>> set n [vecnorm [expr 0.5*[vecsub $coords($id2) $coords($id3)]]]
>>
>># get coords of pulled atom
>>
>> set r $coords($id1)
>>
>> # get the new x,y,z components and calculate the force
>>
>> set x1 [lindex $r 0]
>> set y1 [lindex $r 1]
>> set z1 [lindex $r 2]
>>
>> set nx [lindex $n 0]
>> set ny [lindex $n 1]
>> set nz [lindex $n 2]
>>
>> set vx [expr $v*$nx]
>> set vy [expr $v*$ny]
>> set vz [expr $v*$nz]
>>
>> # calculate forces
>>
>> set fx [expr $k*($x0+$vx*$t-$x1)]
>> set fy [expr $k*($y0+$vy*$t-$y1)]
>> set fz [expr $k*($z0+$vz*$t-$z1)]
>> lappend f $fx $fy $fz
>>
>> # add forces
>>
>> addforce $id1 $f
>>
>> # set the output
>>
>> set foo [expr $t % $Tclfreq]
>> if { $foo == 0 } {
>> set outfile [open $outfilename a]
>> set time [expr $t/1000.0]
>> puts $outfile "$time $r $f"
>> close $outfile
>> }
>> incr t
>> return
>>}
>>
>>
>>
>>
>>--
>>----------------------------------------------------------------------------
>>Dr. Vlad Cojocaru
>>
>>EML Research gGmbH
>>Schloss-Wolfsbrunnenweg 33
>>69118 Heidelberg
>>
>>Tel: ++49-6221-533266
>>Fax: ++49-6221-533298
>>
>>e-mail:Vlad.Cojocaru[at]eml-r.villa-bosch.de
>>
>>http://projects.villa-bosch.de/mcm/people/cojocaru/
>>
>>----------------------------------------------------------------------------
>>EML Research gGmbH
>>Amtgericht Mannheim / HRB 337446
>>Managing Partner: Dr. h.c. Klaus Tschira
>>Scientific and Managing Director: Prof. Dr.-Ing. Andreas Reuter
>>http://www.eml-r.org
>>----------------------------------------------------------------------------
>>
>>
>>
>>
>>
>
>
>
-- ---------------------------------------------------------------------------- Dr. Vlad Cojocaru EML Research gGmbH Schloss-Wolfsbrunnenweg 33 69118 Heidelberg Tel: ++49-6221-533266 Fax: ++49-6221-533298 e-mail:Vlad.Cojocaru[at]eml-r.villa-bosch.de http://projects.villa-bosch.de/mcm/people/cojocaru/ ---------------------------------------------------------------------------- EML Research gGmbH Amtgericht Mannheim / HRB 337446 Managing Partner: Dr. h.c. Klaus Tschira Scientific and Managing Director: Prof. Dr.-Ing. Andreas Reuter http://www.eml-r.org ----------------------------------------------------------------------------
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