From: Jacqueline Schmidt (jacqueline_schmidt_1983_at_yahoo.com)
Date: Thu Feb 28 2013 - 01:12:36 CST
Dear Norman,
Thanks a lot for your answer. As you suggested, I am now trying to fix the lower part of my surface.
I have a general question, maybe a bit primitive. If I have the surface fixed (partly or all of it), then why should I add the same force (but in the opposite direction) as added to the peptide to the surface? Is this because of conservation of energy?
Thanks again for your help
jackie
________________________________
From: Norman Geist <norman.geist_at_uni-greifswald.de>
To: 'Jacqueline Schmidt' <jacqueline_schmidt_1983_at_yahoo.com>
Cc: Namd Mailing List <namd-l_at_ks.uiuc.edu>
Sent: Thursday, February 28, 2013 1:48 AM
Subject: AW: namd-l: smd simulation
Hi Jaqueline,
we also work with surfaces. If your surface has multiple layers,
it’s enough maybe to just fix one of them, maybe the one that is the most
far away from the peptide. Possibly fixing some single atoms within the surface
would also do the job. Not to fix anything would require a pulling force of the
surface in the opposite direction to the same m/s value. As you say you got constant
velocity, you just need to get a pulling force for the surface which equals the
same speed for the surface, or? Additionally, why not fix one atom of the
peptide, and just pull the surface?
Norman Geist.
Von:owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag von Jacqueline
Schmidt
Gesendet: Mittwoch, 27. Februar 2013 15:28
An: namd
Betreff: namd-l: smd simulation
Dear NAMD
users,
I am
trying to perform a smd md on a peptide which is adsorbed to a mineral surface.
For this purpose I added a constant velocity to the peptide atoms trough tcl
interface. To make the surface not moving upwards I added a smd velocity equal
to zero with a very large arbitrary force constant (I don't want to fix the
surface coordinates; I want the atoms in the surface remain flexible but at the
same time not move upwards with the peptide). However, despite the very large
force constant for the surface, it is still moving upward in some occasions
along with the peptide. Does anyone has experience on these type of simulations?
I appreciate any comments (my question was how to prevent surface from moving
upward without fixing its coordinates)
Thanks, jackie
************Here is the conf file
, smd section************
# SMD settings #this is applied on
the surface
if {1} {
SMD
on
SMDFile
smd_ref.pdb
SMDk
10000
SMDVel
0.000
SMDDir
1 1 1
SMDOutputFreq
100
}
# Tcl interface #this is applied
on the peptide
if {1} {
tclForces
on
tclForcesScript
smd.tcl
}
********Here is the tcl
script**************************
#define a group including the
peptide atoms
set grp2 {}
for {set j 1 } { $j <=90 }
{incr j } {
lappend grp2 $j
}
set a2 [addgroup $grp2]
# set the output frequency,
initialize the time counter
set Tclfreq 10
set
t 0
# force constant (kcal/mol/A^2)
set k 20
# pulling velocity (A/timestep)
set v 0.0000025
set outfilename rklpda_smd_tcl.out
open $outfilename w
set r20z 31
proc calcforces {} {
global Tclfreq t k v a2
r20z outfilename
loadcoords coordinate
set r2 $coordinate($a2)
set r2x [lindex $r2 0]
set r2y [lindex $r2 1]
set r2z [lindex $r2 2]
if { $t == 0 } {
set r20z $r2z
}
set f2x 0
set f2y 0
set f2z [expr $k*($v*$t-$r2z+$r20z)]
lappend f2 $f2x $f2y $f2z
addforce $a2 $f2
set foo [expr $t %
$Tclfreq]
if { $foo == 0 } {
set outfile
[open $outfilename a]
# calc time in ps
set time
[expr $t]
puts $outfile
"$time $r2z $f2z"
close
$outfile
}
incr t
return
}
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