[gmx-users] dihedral

[Prasad Gajula]

Dear Gromacs users,
Thanks a lot for your input so far.

my problem regarding the dihedral angle still suffering me. I need to
rotate a bond by certain angle, say from 30 to 150 degrees. i would like
to see how the peptide will change its conformation for example CIS to
TRANS by the rotation. I tried to use as chris suggested below. but could
not see any rotation around the bond. It is just fluctuating around its
original bond but not rotating. can u help me.

Thanks and regards
Gajula

>For example, my peptide is rotating 50 degrees about a bond B-C, out of
>four bonded atoms A-B-C-D.  I want to apply additional force on this
> dihedral(B-C) during my simulation(only for this particular atoms to
>make it rotate further till 180 degrees). All the remaining atoms in
the >peptide will have normal force as usual.
> May I ask you, how can I apply this in gromacs code.
> Any help will be appreciated!

The current manual is good at describing what the options do for
dihedral restraints, but (to my knowlegde) doesn't explain at all how
to get the implementation up and running. Here is how I have done it
based on searching the mailing list for answers. I suggest that
something like this is added by way of example to the manual for
future releases.

Also, the manual is a bit unclear about whether this type of dihedral
restraint is stable for use near 180deg. I have found that for my
system everything appears to behave normally and as expected over the
entire range of dihedral angles including 180deg.

In your .top file:

; Include forcefield parameters
#include "ffoplsaa.itp"
; Include topologies
#include "myprotein.itp"
[ dihedral_restraints ]
; ai   aj    ak    al  type  label  phi  dphi  kfac  power
    A    B     C     D     1      1  180     0     1      2
#include "tip4p.itp"
etc...
Make sure that the dihedral_restraints section comes immediately after
the inclusion of the protein topology. If you have the protein
topology directly in your .top file then just include
dihedral_restraints after the protein listing but before any mention
of things that are not that protein molecule.

Add this to your .mdp
;dihedral restraints
dihre               =  simple
dihre_fc            =  100     ; or whatever value you desire
dihre_tau           =  0.0
nstdihreout         =  50

For more information about what these options mean, please refer to
the manual.