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

[Dr. Vitaly V. G. Chaban]

> 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?
>
>  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

Himanshu -

I would look for a problem in the atom numbers in your restraints. If
something ususual happens (the simulation crashes), then the option
works. If it works, the MDP file is most likely correct. The only
other candidate is a topology file...

Vitaly

Dr. Vitaly V. Chaban, 430 Hutchison Hall
Dept. Chemistry, University of Rochester
120 Trustee Road, Rochester, NY 14627-0216
THE UNITED STATES OF AMERICA