[gmx-users] bilayers move apart by nanometers upon implementing dihedral restraints on lipid tails

[Justin A. Lemkul]

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

========================================