[gmx-users] RE: vsite problem in gromacs 4.0

chris.neale at utoronto.ca chris.neale at utoronto.ca
Tue Nov 4 16:48:16 CET 2008

1) Are whole charge groups are utilized also for LJ calculation if one  
atom of that charge group falls within the cutoff? If so, it seems to  
me that putting all of the atoms in each aromatic side chain into  
their own charge group could slightly change the equilibrium  
properties of a peptide or protein since aromatic residues would then  
be more strongly attracting near the cutoff distance than they are  
when assigned the regular charge groups of a force-field. Probably not  
a serious issue, but something to consider.

2) Also, Berk, you mention the possibility for "dt=4 or 5 fs with  
-vsite h (and optionally heavy hydrogens)". I am a little confused  
again. I interpreted, based on some help that you gave me last week,  
that the following should be enough:

pdb2gmx -vsite, with:
dt = 0.004
constraints =  all-bonds
constraint_algorithm =  lincs
lincs-iter =  1
lincs-order =  6

And that to go above dt=0.005 would require heavy hydrogens also,  
although that might not be such a good idea.

your post: http://www.gromacs.org/pipermail/gmx-users/2008-October/037569.html

Thanks for any clarifications,

-- original message --

You can not do much.
The reason for this error message is also valid for older versions.
It can not be guaranteed that the virtual sites in one charge group will
have the same periodic shift. But before 4.0 there was no check for this.

I would simply not use vsite aromatics. I am in favor of completely
removing this option from pdb2gmx, since you do not gain so much
compared with dt=4 or 5 fs with -vsite h (and optionally heavy hydrogens).

If you really want to use the vsite aromatics, you can put all atoms
in the aromatic groups in separate charge groups, but that will make
the simulation slightly slower.


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