On 7/5/12 10:25 AM, himanshu khandelia wrote:
I am trying to implement dihedral restraints for lipids in a bilayer
using what is suggested here:
http://www.gromacs.org/Documentation/How-tos/Dihedral_Restraints
However, although the dihedral angles seem to be restrained fine, the
leaflets move apart by 10s of nanometers along +z over a nanosecond or
so, after which of course, the simulation crashes.
Can anyone suggest what I might be doing wrong?
Are the simulations stable in the absence of these restraints? Are you sure
this isn't just a matter of periodicity creating the illusion of large-scale
diffusion?
-Justin
version 4.5.4
In the mdp file:
;dihedral restraints
dihre = yes
dihre_fc = 100
In the topology:
[ dihedral_restraints ]
17 18 19 20 1 1 100 0 1 2
18 19 20 21 1 1 100 0 1 2
19 20 21 22 1 1 100 0 1 2
20 21 22 23 1 1 100 0 1 2
21 22 23 24 1 1 100 0 1 2
...
etc.
Himanshu
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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