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