[gmx-users] How to fix four different atoms of diffrent residue in tetrahedral geometry while MD.

[Anton Feenstra]

Anil Kumar wrote:

> Hi,
> 
> I wnat to do MD of 16mer polypeptide with fixed  tetrahedral geometry of
> four different atoms of four different residue.
> 
> I donot understand how to give distance restrain to fix these four atoms.
> 
> I tried dis_rest.itp
> 
> [distance_restraints file]
> ; ai    aj      type    index   type'   low     up1     up2     fac
> 22      61      1       0       1       0.310   0.335   0.345   1
> 22      109     1       1       1       0.310   0.335   0.345   1
> 22      148     1       1       1       0.310   0.335   0.345   1
> 61      109     1       1       1       0.310   0.335   0.345   1
> 61      148     1       1       1       0.310   0.335   0.345   1
> 109     148     1       1       1       0.310   0.335   0.345   1
> 
> I have included this in corresponding top file.
> 
> ; Include Position restraint file
> #ifdef DIS_REST
> #include "dis_rest.itp"
> #endif

You will have to say 'defines = -DDIS_REST' in your .mdp file.


-- 
Groetjes,

Anton

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|  _   _  ___,| K. Anton Feenstra                                     |
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