[gmx-users] bond, angle and dihedral restraints in Gromacs
Rebeca García Fandiño
regafan at hotmail.com
Thu May 21 18:22:38 CEST 2009
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.
Dr. Rebeca Garcia
Parc Cientific de Barcelona
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