Re: Re: How to obtain the system force on a fixed atom

From: Jian Liu (bay__gulf618_at_sina.com)
Date: Mon Dec 21 2009 - 07:34:30 CST

Dear everyone

To Mary:
I do not think it's a good idea to act large homonic force to some atoms.
It's indeed the amplitude decreased underlarge homonic force, analyzed from Newton's law;
But the oscillation period of this atom would increased at the same time. If this is smaller than the ten times of timestep, the simulation would become unstable.

To Jerome:
Not only the "loadforces", but the "loadcoords" and "loadmasses" are failed in windows_namd2.7b1/2 .

best,
Jian Liu
------------------------------------------------
Jian Liu
Master-degree graduate candidate majoring in Molecular Modelling
Department of Physical Chemistry & Chemical Physics
College of Chemistry, Chemical Engineering and Materials Science
Soochow University
Suzhou 215123, China
http://groups.google.com/group/bay__gulf618?hl=zh-CN
----- Original Message -----
From: Jérôme Hénin <jhenin_at_ifr88.cnrs-mrs.fr>
To: chengh_at_ringo.chem.pitt.edu
Subject: Re: namd-l: How to obtain the system force on a fixed atom
Date: 2009-12-17 00:38:55

Dear Mary,

Does the fixedAtomsForces option make a difference in the behavior you see?

The stiff harmonic restraint is not a problem per se, as long as the

simulation remains stable, but the bad interaction with fixed atoms

could be a fixable bug. I don't remember whether the case was

considered when those TclForces functions were added.


As far as I know, you are the first to report the problem with

load(total)forces in NAMD 2.7b1. That's interesting, and should

certainly be addressed. Can you check that it still happens with

version 2.7b2, and describe the unexpected behavior precisely?


Best,

Jerome


2009/12/16 <chengh_at_ringo.chem.pitt.edu>:

> Dear NAMD developers and users,

>

> Does anyone know how to get the system force on a fixed atom. I used

> tclForces "loadtotalforces". It returned a value of zero. To solve this

> problem, I used a very large homonic restraint (K=100000.0) to mimic

> "fixed". Then using "loadforces" and "loadtotalforces" together to get the

> system force. Any better solutions?

>

> By the way, I noticed that "loadtotalforces" or "loadforces" did not work

> using NAMD 2.7b1. I have to use an older version NAMD 2.6 to make it work.

> I attached the script I used. Can anybody fix this problem in NAMD 2.7b1?

>

> Many thanks,

>

> Mary H. Cheng

> Department of Chemistry

> University of Pittsburgh

>

> ##############################################################################

> tclForces on

> tclForcesScript {

>  set aid1 168200

>  addatom $aid1

>  set Tclfreq 10

>  set k 100000.0

>  set x0 3.706

>  set y0 1.398

>  set z0 -26.642

>

>  proc calcforces {} {

>  global aid1 Tclfreq

>  global k z0 x0 y0

>

>  set t [getstep]

>  loadcoords r

>  set rx [lindex $r($aid1) 0]

>  set ry [lindex $r($aid1) 1]

>  set rz [lindex $r($aid1) 2]

>  print "COORDs: $t $r($aid1)"

>

>  addenergy [expr

> $k*($rx-$x0)*($rx-$x0)/2.0+$k*($ry-$y0)*($ry-$y0)/2.0+$k*($rz-$z0)*($rz-$z0)/2.0]

>  set force "[expr -$k*($rx-$x0)] [expr -$k*($ry-$y0)] [expr

> -$k*($rz-$z0)]"

>  addforce $aid1 $force

>

>  loadtotalforces fortot

>  loadforces forc

>

>  if { [array exists forc] } {

>  set f1 $forc($aid1)

>  set f1x [lindex $f1 0]

>  set f1y [lindex $f1 1]

>  set f1z [lindex $f1 2]

>  print "ADDforce: $t $f1x $f1y $f1z"

>

>  }

>  if

> {

> [array

> exists

> fortot]

> }

> {

>  set ftot $fortot($aid1)

>  set ftotx [lindex $ftot 0]

>  set ftoty [lindex $ftot 1]

>  set ftotz [lindex $ftot 2]

>  print "TOTforce: $t $ftotx $ftoty $ftotz"

>  print "SYSforce:$t [expr $ftotx-$f1x] [expr $ftoty-$f1y] [expr

> $ftotz-$f1z]"  }

>

>

>  }

>

>

> }

>

>

>

>


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