Lara Bunte wrote:
Hi
After pdb2gmx I got two [ dihedrals ] sections in the topology file.
[ dihedrals ]
ai aj ak al funct c0 c1 c2
c3 c4 c5
2 1 19 8 5
6 8 9 10 5
6 8 19 1 5
[ dihedrals ]
ai aj ak al funct c0 c1 c2
c3
1 8 6 4 2 180 100
1 2 4 5 2 180 100
1 10 11 13 2 180 100
Why is pdb2gmx doing this? I commented the first block out. Is this allowed?
You can comment anything out that you like, but if you don't know what you're
doing you're likely to completely break the physical model. Note the function
types (which are explained in the manual). The first directive indicates
Fourier dihedrals (a type of proper dihedral) while the second indicates
improper dihedrals.
-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
========================================
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
