Lara Bunte wrote:
Hi
The first part in a .rtp file is the [ bondedtypes ] with syntax
[ bondedtypes ]
; bonds angles dihedrals impropers
1 1 1 2
1.)
What do this numbers mean? I found nothing in the manual to that.
They are the function types for these different interactions. Function types
are listed in Table 5.5.
2.)
If you have improper dihedrals, do you really nead both in this section? Why not only impropers?
The order of the function types must be adhered to so that the parameters are
properly interpreted. Check gmx.ff/aminoacids.rtp for a complete description of
each of the 8 possible columns and the order that they must follow.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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