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

Berk Hess gmx3 at hotmail.com
Tue Nov 4 17:02:00 CET 2008

> Date: Tue, 4 Nov 2008 10:48:16 -0500
> From: chris.neale at utoronto.ca
> To: gmx-users at gromacs.org
> Subject: [gmx-users] RE: vsite problem in gromacs 4.0
> 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.

Most force fields (except GROMOS) have probably been parametrized
without charge groups.
Therefore having smaller charge groups is always more accurate, unless you
have a buffer region, which is now possible in 4.0. (This all assumes that
you use PME and not cut-off or reaction-field for electrostatics)
This is indeed not a serious issue.

> 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.

Using 5 fs without heavy hydrogens will not cause stability problems.
It might cause slightly less accurate integration. But these integration
errors are usually much smaller than other errors, such as cut-off errors.
It is all a matter of what accuracy you want.
If you want to be sure, you can run simulations with a 4 and 5 fs timestep
(do not forget to modify nstlist as well, so the neighborlist update frequency
stays constant) and then check if the properties you are interested in change.
For many properties this might not be feasible, since you can not converge
the properties within reasonable time.

In our experience 5 fs works fine. I would not hesitate to use it for large
systems, where one can anyhow not sample all conformational space.
I am currently mainly doing accurate calculations of thermodynamic quantities,
for these I use 4 fs.


> your post: http://www.gromacs.org/pipermail/gmx-users/2008-October/037569.html
> Thanks for any clarifications,
> Chris.
> -- 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.
> Berk
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