From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Sat Oct 17 2009 - 00:56:45 CDT
Yes, you can. But it will only work in 1D as you've proposed, e.g., not n =
(1,1,1).
Regarding your initial question, see the addenergy term in the manual:
http://www.ks.uiuc.edu/Research/namd/2.7b1/ug/node43.html
-----Original Message-----
From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On Behalf
Of Seungho Choe
Sent: Saturday, October 17, 2009 12:21 AM
To: Seungho Choe
Cc: namd-l_at_ks.uiuc.edu
Subject: Re: namd-l: tcl force
Hi,
I wonder whether I can use SMD with v=0, n= (0,0,1) to restrain the
center of mass of a molecule in z direction ?
It seems that in this case I don't need to worry about the energy term
that I mentioned in the previous my post. Could someone clarify this ?
Apology if this issue was already discussed before.
Best,
Seungho
Seungho Choe wrote:
> Dear all,
>
> I'm trying to restrain the center of mass (only z position) of a
> molecule. Below is my tcl script. What I'm wondering is whether a new
> energy term from the added force is applied correctly to the total
> energy. Do I need to explicitly add the energy term in the script ? Is
> there any way to check this ? Any comments are welcome. Thank you in
> advance.
>
> Best,
> Seungho
>
> ************************************************************************
> set numatoms 63230
>
> set atoms {}
> for {set i 63207} { $i <= $numatoms} { incr i} {
> lappend atoms $i
> }
>
> print "atoms:$atoms"
>
> foreach atom $atoms {
> addatom $atom
> }
>
> set groupid [addgroup $atoms]
>
>
> # Set spring constant
> set k 7.0
> set z0 -3
>
> proc calcforces {} {
>
> global atoms groupid numatoms k z0
> loadcoords p
>
> #print "$p($groupid)"
>
> set z1 [lindex $p($groupid) 2]
>
> print "z comp:$z1"
>
> set r01 [expr $z1-$z0]
> #print "r01:$r01"
>
> if {$r01 > 0} {
> set n01 {0 0 -1}
> } elseif {$r01 < 0} {
> set n01 {0 0 +1}
> }
>
> # Calculate the "force"
> set force [expr abs($k*$r01)]
>
> set forcez [vecscale $force $n01]
>
> print "forcez:$forcez"
>
> addforce $groupid $forcez
>
> }
>
>
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