Vitaly V. Chaban wrote:
Justin,
Thanks. These tidbits are too difficult for my brain to understand.
Let's make the things easier. One has the below compound.
7 - 1 - 2
/ \
6 3
\ /
5 - 4
I want the atom 7 to be located in the same plane with atoms 1 2 and
6. Then in topol.top:
[ dihedrals ]
atoms func angle constant
1 2 6 7 2 180 4.602
If this is the appropriate syntax for whatever force field you are using, yes.
The reference atom is 1, and is held in a plane defined by 7, 2, and 6. If atom
7 is part of a planar group, you need to define a separate improper for it.
I mention the syntax because the order of atoms is different between, e.g.,
Gromos and OPLS (as are the implementations of the forms of the dihedrals).
Will this line do what I want here?
Try it and see :)
-Justin
Vitaly
On Wed, Sep 23, 2009 at 1:53 PM, Vitaly V. Chaban <[email protected]> wrote:
Hi,
I have got confused with setting up improper dihedrals in the gromacs
topologies. In the manual (ver. 4.0) I see the section named [
impropers ] (page 104)
"
[ impropers ]
C O1 O2 CA
"
but in the example system of the peptide
(share/gromacs/tutor/speptide) one finds defining impropers using the
second (in the same file) [ dihedrals ] section.
[ dihedrals ]
; ai aj ak al funct c0 c1
c2 c3
1 23 5 6 1 improper_X_X_C_X
1 23 5 7 1 improper_N_A_C1_C
2 5 1 3 1 improper_X_X_M3_X
2 5 1 4 1 improper_X_X_M3_X
What is the correct way to work with improper dihedrals? I have four
sites, then angle value and then one force constant. What should my
topology line look like to accomplish that?
I would also be very grateful if somebody could share some topology
with improper angles to understand how it works.
Vitaly
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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