VMD-L Mailing List
From: Cesar Luis Avila (cavila_at_fbqf.unt.edu.ar)
Date: Fri Sep 01 2006 - 20:02:36 CDT
- Next message: Jim Phillips: "Re: Angles and dihedral generation"
- Previous message: Jan Saam: "Re: looking for VMD draw scripts."
- Next in thread: Jim Phillips: "Re: Angles and dihedral generation"
- Reply: Jim Phillips: "Re: Angles and dihedral generation"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]
Where can I find information on when to generate angles and dihedrals
for different segments?
Throughout internet I have found different ways for generating segments
For water
{first none
last none
auto none }
According to psfgen manual "Because CHARMM uses an additional H-H bond
we must disable generation of angles and dihedrals for segments
containing waters". Does this apply only to TIP3? What about other water
models?
For membranes :
{first none
last none
auto none dihedrals}
This options were used by membrane builder on VMD. Does this also apply
to other lipids like DMPC? Why shouldn't angles be generated in this case?
At last for proteins
{first nter
last cter
auto angles dihedrals}
This options were used by autopsf builder on VMD.
Any help will be very much appreciated.
Regards
Cesar
- Next message: Jim Phillips: "Re: Angles and dihedral generation"
- Previous message: Jan Saam: "Re: looking for VMD draw scripts."
- Next in thread: Jim Phillips: "Re: Angles and dihedral generation"
- Reply: Jim Phillips: "Re: Angles and dihedral generation"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]