[gmx-users] dihedral

Lars.Schaefer at mpi-bpc.mpg.de Lars.Schaefer at mpi-bpc.mpg.de
Sat Jan 6 11:49:27 CET 2007

Dear Prasad,
I did not follow the whole issue, but you could also exploit the fep code
for rotating around a bond. Just define in state A the dihedral potential
such that it has its minimum at, say, 30 deg, and in state B, the dihedral
has its minimum at, say, 150 deg. Then you do a slow growth simulation and
 change from state A to B, this should induce the isomerisation.
Good luck,

> 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.
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