From: Subramanian Vaitheeswaran (vaithee_at_umd.edu)
Date: Thu Jun 21 2007 - 11:29:40 CDT
You can also enforce dihedral restraints using the ABF module. No derivatives are calculated and the additional computational expense appears to be minimal. Here is the ABF part of my configuration file:
#############################################################
## ABF ##
#############################################################
if {1} {
source ~/NAMD_2.6_Linux-i686/lib/abf/abf.tcl
abf coordinate distance-com
abf abf1 {1 2 3 4 5 6 7 8 9 10 11 12 13 14 15}
abf abf2 {16 17 18 19 20}
abf dxi 0.1
abf xiMin 3.5
abf xiMax 30.5
abf outFile abf_AA.pmf
abf historyFile abf_AA.hist
abf fullSamples 200
abf inFiles {}
abf dSmooth 0.0
abf restraintList {
Dih.1 {dihe {AA 1 CD1} {AA 1 CE1} {AA 1 CZ} {AA 2 C} 40. 90.}
Ang.1 {angle {AA 1 CG} {AA 1 CZ} {AA 2 C} 40. 90.}
}
}
On 6/19/07, maria goranovic <mariagoranovic_at_gmail.com> wrote:
>
> I want to restrain about 20 random coil contiguous residues to a helical
> conformation, while leaving the rest of my protein intact. According to the
> documentation, there are at least three ways to do this:
>
> 1. Using a tcl forces script, like the one recommended in the manual.
> http://www.ks.uiuc.edu/Research/namd/2.6b1/ug/node32.html#SECTION00096700000000000000.
> However, the script may get slightly tedious for 20 operations.
> 2. Using the restraining options in the free energy methods. But here, the
> free energy routines will need to be invoked, which might slow the overall
> calculation, because an unnecessary derivative will be calculated each step.
>
> 3. Modify the psf to define new residue types and new dihedrals (I want to
> avoid this).
>
> My questions:
>
> a. Which is the recommended method in terms of saving of computational
> time ?
> b. In the free energy method, is the dihedral restrained harmonically
> throughout the simulation like it would be in the TCL forces script ?
> c. In terms of added potentials and forces, is the effect of using a tcl
> forces script or a restraint in a free energy calculation similar to that,
> say of using standard harmonic constraints in NAMD ?
>
> My goal is to investigate the effect of the coil-helix transformation on
> the loop region next to the protein region in question.
>
> Any suggestions please ? All partial answers are also welcome :)
>
> -Maria
>
> --
> Maria G.
> Technical University of Denmark
>
-- Maria G. Technical University of Denmark Copenhagen
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