From: Chris Chipot (Christophe.Chipot_at_edam.uhp-nancy.fr)
Date: Mon Oct 29 2007 - 13:22:52 CDT
Dear Vlad,
I suggest that you also check the following webpage:
http://www.edam.uhp-nancy.fr/ABF/
which provides an overview of ABF and the extent of its field of
applications.
Chris Chipot
Vlad Cojocaru a écrit :
> 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
>>> ----------------------------------------------------------------------------
>>>
>>>
>>>
>>>
>>>
>>
>>
>>
>
--
_______________________________________________________________________
Chris Chipot, Ph.D.
Equipe de dynamique des assemblages membranaires
Unité mixte de recherche CNRS/UHP No 7565
Nancy Université Phone: +33 (0)3-83-68-40-97
B.P. 239 Fax: +33 (0)3-83-68-43-87
54506 Vandœuvre-lès-Nancy Cedex
E-mail: Christophe.Chipot_at_edam.uhp-nancy.fr
http://www.edam.uhp-nancy.fr
Science without management is worse than management without science
N. G. van Kampen
_______________________________________________________________________
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