[gmx-users] bond, angle and dihedral restraints in Gromacs

[Rebeca García Fandiño]

Hello,
I would like to simulate a CNT and I want to apply a harmonic potential:
-on the C-C bonds 
-on the bond angles 
-on the dihedral angles
with a different spring constant for each case.

I have read Section 4.3 from Gromacs manual, but I actually have some doubts about how to include this in the topology.

-for the distance restraints I have tried to use genrestr: 

genrestr -f cnt_wat_gmx_centered.gro -o posre_dist.itp -disre -fc 400000

 The file I obtain is something like:

; distance restraints for UNK of cnt_wat_gmx.gro created by rdparm2gmx.pl Wed May 20 10:20:59 BST 2009

[ distance_restraints ]
;   i     j ? label      funct         lo        up1        up2     weight
    1     2 1     0          1   0.403354   0.603354    1.60335          1
    1     3 1     1          1   0.587676   0.787676    1.78768          1
    1     4 1     2          1   0.769212   0.969212    1.96921          1
    1     5 1     3          1    0.86081    1.06081    2.06081          1
(...)

This is different from the [distance_restraint] example shown in pag 69 of the manual, now I don' t have the fac column. I would like to apply a spring constant of 400000 to C-C bonds, but where is the constant here? How could I apply a determined spring constant? In the .mdp file? Besides, all the distances are restrained... Is there any way to restrain only the C-C bonds? I mean I don' t want to restrain the distance between a carbon and a carbon far away from it, only restraining the neighbouring carbons to a distance of 1.4 A.

Another question is: Is there any tool to construct the equivalent angle_restraints and dihedral_restraints in an authomatic way, or should I do it by hand?

Thank you very much in advance for your help.

Best wishes,

Dr. Rebeca Garcia
Parc Cientific de Barcelona
Spain






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