From: maria goranovic (mariagoranovic_at_gmail.com)
Date: Thu Jul 12 2007 - 08:11:55 CDT
Thank you Peter,
In yesterday's post, you mention that you use the following strategy:
"Use a compiled tcl extension (probably written in C and built using
swig) to do any serious math in the tclforces script "
Can you please elaborate on this ? How is this done ?
Secondly, how does the CVS work ? I understand that I have to apply for an
account, install CVS on my local computer. What then ? Do I need to make
changes in the source code to enable this extrabonds feature ? Or do I just
need to use a beta binary and use the extrabonds feature ?
Thank you a lot,
> On 7/12/07, Peter Freddolino <petefred_at_ks.uiuc.edu> wrote:
> > Maria,
> > please see the discussion from yesterday on this error. The same
> > solutions apply to your case.
> > Alternatively, if you don't mind using the cvs version of namd, you can
> > try the new extrabonds feature, which allows you to specify a file
> > containing dihedral restraints of the format
> > dihedral index1 index2 index3 index4 k theta0
> > To use this feature, set
> > extraBonds yes
> > extraBondsFile FILENAME
> > (where filename is the file containing your dihedral definitions)
> > in your config file.
> > Peter
> > maria goranovic wrote:
> > > While using a tclforces script to apply dihedral restraints, I get the
> > > following error after about 85000 steps of dynamics.
> > >
> > > #=============================================
> > > WRITING COORDINATES TO DCD FILE AT STEP 87000
> > > TCL: force not a vector
> > > FATAL ERROR: force not a vector
> > > while executing
> > > "addforce $id21 [vecscale $g5 $forcepsi]"
> > > (procedure "calcforces" line 78)
> > > invoked from within
> > > "calcforces"
> > > #==============================================
> > >
> > > The constraint script is attached. The attempt is to constrain the
> > > dihedral angles of the residues 19 and 197 to helical values.
> > >
> > > There is some discussion in the mail archive about the "force not a
> > > vector" error. What is confusing is why the error shows up only after
> > > 85000 steps, and not from the very beginning of the simulation ?
> > >
> > > Can someone please suggest a remedy ?
> > >
> > > -Maria.
> > > --
> > > Maria G.
> > > Technical University of Denmark
> > > Copenhagen
> Maria G.
> Technical University of Denmark
-- Maria G. Technical University of Denmark Copenhagen
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