From: P.-L. Chau (pc104_at_pasteur.fr)
Date: Mon May 07 2012 - 20:59:14 CDT
Thanks for your message.
> Does the atom numbers printed match your wanted CA atoms?
Yes.
> Do you start from a unwrapped restart?
Yes.
> Does namd use other unit for the coords internally?
> ->If someone know, please tell us.
I do not quite know what that means. Could you perhaps expound?
> Does namd for some other reason than wrapping updates the coordinates
> initially?
No.
Anyway, I have got the script working, and it looks like this:
[...]
wrapmode input
proc calcforces {step unique Rrate Rtarget K} {
global aalist
if {$unique} {
if { $step == 20000001} {puts "K = $K"}
}
if {$unique} {puts "****** step = $step"}
while {[nextatom]} {
set atomid [getid]
if { [lsearch $aalist $atomid] >= 0 } {
set rvec [getcoord]
if {$unique} {puts "$atomid $rvec"}
foreach { x y z } $rvec {break}
set fX [expr $K * $x * ($step-20000000) ]
set fY [expr $K * $y * ($step-20000000) ]
set fZ [expr 0.0]
puts "****** $atomid x- and y-force = $fX $fY"
addforce "$fX $fY $fZ"
}
}
}
Obviously this is not what I would use in my research, but I can now add
artificial forces to push designated atoms in specified directions.
Thank you very much to you all who helped me with this.
Best regards,
P-L Chau
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