Re: phi and psi dihedral restraints

From: luca (bellucci14_at_unisi.it)
Date: Mon Oct 23 2006 - 15:07:25 CDT

Hi all,
I think There are some question about internal coordinates constraint that are
not " clear ".
Internal Coordinates IC are : bond angle torsion....
My personal opinion are:
1- One can add whichever coordinates in CHARMM topology procedure.
    In this case there are some problem due to automatic generation of psf
    file and standard parameter.....
2 Improper torsion has not automatic procedure therefore is good choice for
    model your system, if it is possible...
3 One can add/delete bond or other internal coordinates
    (bond,angle,torsion....) directly in psf file,
    but .... you know what do you make?
4 In standard molecular dynamics (NVE NPT....) you can modify force with
   tclforce script ( see manual). With this procedure you can edit "source
   code" for your force type....
   F = -dV/dx = -dv/dq*dq/dx etc......
   see attach for stretching example
5 There are some type of position constrain... see manual.. these are very
   simple.
6 There are some type of constrains that are
    correlates to free energy calculation, but I do not know if they always
    work.....do you know? I have not understood as they work.


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