[gmx-users] Two-body Bonded Distance

Justin Lemkul jalemkul at vt.edu
Sat Mar 1 04:25:00 CET 2014

On 2/28/14, 4:36 PM, jolayfield 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.

What exactly is the problem?  The output looks totally normal - mdrun has 
identified a 1-4 interaction between CB and CE, which should exist.  Are you 
saying that this outcome is dependent upon inclusion of a virtual particle?



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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