[gmx-users] Ryckeart Bellemans parameters for Fe coupled to cystines

Dallas Warren dallas.warren at vcp.monash.edu.au
Tue Dec 16 00:10:01 CET 2003

>Thanks for the suggestion Dr Warren. I tried what you
>suggested ,ie, removing the 1-4 interaction pairs for
>the troubling hydrogens but even this doesn't seem to
>work and i get the lincs error again for the same
>hydrogens ..does it has to do something with the RB
>dihedrals ? Currently I have specified the dihedrals
>for these hydrogens as proper .

If you have a RB defined for a particular dihedral then you have to remove 
the 1-4 interactions anyway.  If instead the dihedral is defined as a 
proper or improper then in most cases the 14 should be there.

I would look around the bond to see what would be making it move so 
quickly.  Large charges can do that.  Also whether you are using too larger 
time step.

Another trick to slow down the motion of atoms (which is mentioned in the 
manual as well) is to increase the mass of the hydrogens by a factor of 4, 
then subtract the additional mass of the atom it is attached to.

Catch ya,

Dr. Dallas Warren
Research Fellow
Department of Pharmaceutical Biology and Pharmacology
Victorian College of Pharmacy, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at vcp.monash.edu.au
+61 3 9903 9083
When the only tool you own is a hammer, every problem begins to resemble a nail.
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