[gmx-users] Two-body Bonded Distance

jolayfield jolayfield at gmail.com
Fri Feb 28 22:37:26 CET 2014

   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

View this message in context: http://gromacs.5086.x6.nabble.com/Two-body-Bonded-Distance-tp5014864.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.

More information about the gromacs.org_gmx-users mailing list