[gmx-users] Two-body Bonded Distance

Mark Abraham mark.j.abraham at gmail.com
Mon Mar 3 05:28:50 CET 2014

Beta and epsilon carbon atoms in straight-chain acids do not share a bond,
by definition. Are you describing the virtual site that you think you are
On Feb 28, 2014 10:43 PM, "jolayfield" <jolayfield at gmail.com> wrote:

>    I am trying to calculate the electrostatic field at the midpoint of a
> bond
> during an MD simulation.  To achieve this I equilibrate my protein
> structure
> and then adding a virtual particle at the midpoint of the bond by hand.
> This particle has no non-bonding interactions with other particles and I
> have confirmed that the simulations are reproducible with and without
> incorporating the virtual particle.
>    The problem that I am running into is that when I add the virtual
> particle The calculated two-body bonded interactions are too long by a
> factor of 4.  This limits the number of processors that I can use with
> domain decomposition due to minimum cell size.
> Here is the relevant information from the log file:
> Initial maximum inter charge-group distances:
>     two-body bonded interactions: 1.545 nm, LJ-14, atoms 662 670
>   multi-body bonded interactions: 0.429 nm, Proper Dih., atoms 662 670
> Minimum cell size due to bonded interactions: 1.699 nm
> The atoms are the beta and epsilon carbons from a methionine residue.  I
> have run into this problem over multiple trajectories and it always occurs
> between the CB and CE of different methionine residues.
> Is this a known issue or can anyone provide any help to me?
> I have run this on version 4.5.4 but also checked it on 4.6.3 with the same
> problem.
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