From: Seungho Choe (sec53_at_pitt.edu)
Date: Sun Oct 18 2009 - 20:59:43 CDT
What I see in the manual is that "addenergy" is optional for normal runs.
However, if I want to explicitly see the additional energy term, then I
need to add "addenergy" as you mentioned.
Is this what you meant ?
Thanks,
Seungho
JC Gumbart wrote:
>
> From my reading of the manual, you do have to manually add the energy,
> in addition to the force.
>
>
>
> I think your tcl script is fine, except it's more complicated than
> necessary. The force is just F = -k * (z-z0); you don't need to set
> conditions on r0.
>
>
>
>
>
> *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 1:08 PM
> *To:* JC Gumbart
> *Cc:* namd-l_at_ks.uiuc.edu
> *Subject:* Re: namd-l: tcl force
>
>
>
> Hi JC and NAMD users,
>
> I'm trying to compare both methods: tcl force & SMD.
> Could you please look at my tcl script again and tell me whether it is
> correct ?
> I wonder whether I'm missing some factors in the script. Thanks a lot.
>
> Best,
> Seungho
>
> JC Gumbart wrote:
>
> 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> [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 <mailto: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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