Yanmei Song wrote:
[ dihedrals ]
; ai aj ak al fu c0, c1, m, ...
1 2 5 6 1 0.0 3.77 3 0.0 3.77 3 ; dih CAA
CBF OAW CBH
2 5 6 9 1 0.0 3.77 3 0.0 3.77 3 ; dih CBF
OAW CBH OAY
5 6 9 10 1 0.0 3.77 3 0.0 3.77 3 ; dih OAW
CBH OAY CBJ
6 9 10 13 1 0.0 3.77 3 0.0 3.77 3 ; dih CBH
OAY CBJ OBA
9 10 13 14 1 0.0 3.77 3 0.0 3.77 3 ; dih OAY
CBJ OBA CBL
Sorry to bother you so much times. Above is the real parameter I used
in my top file which probably specified the dihedrals as periodic
(function 1) . But I also used OPLS force field which should read
different parameters as RB. So when the MD runs, does it just read
this parameters in the periodic dihedrals as a RB parameter?
The fifth column determines the functional type used, per the table in
chapter 5 to which I referred you. One can mix and match these at will -
apparently OPLS routinely uses R-B. That doesn't stop you using periodic
ones as well.
If my top
is in a wrong form, how can md runs well and give a good result?
Maybe it does for the observable and time scale you've looked at. One
can't mix force fields and a priori expect the results to be correct.
Extensive testing may reveal an acceptable result. See
http://wiki.gromacs.org/index.php/Parameterization
Mark
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
