[gmx-users] 1-4 Interactions
tsjerkw at gmail.com
Thu Oct 19 09:52:11 CEST 2006
A 1-4 interaction is an interaction between two atoms which are
attached to each other with three bonds in between (two other atoms,
1-2-3-4). Based on the normal bond lengths, angles, etc. two such
atoms should not be further away from each other than 1 nm. Check the
atom locations of 908 and 913 in a viewer and try to see what is wrong
(also check the topology and the box).
On 10/19/06, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> toma0052 wrote:
> > Hello,
> > I am starting simulations on a DPPC lipid bilayer taken from Peter
> > Tieleman's website. Upon trying to run the energy minimization, the
> > program runs, but the results does not appear correct. During the run, I
> > get the warning:
> > Warning: 1-4 interaction between 908 and 913 at distance 1.621 which is
> > larger than the 1-4 table size 1.000 nm. These are ignored for the rest of
> > the simulation. This usually means your system is exploding, if not, you
> > should increase table-extension in your mdp file.
> > I have tried increasing the table-extension in my em.mdp file, but I need
> > to increase it to over 10nm in order for that error to go away. Could
> > someone explain a little bit more on what the table-extension and 1-4
> > interactions are, and what could possibly be wrong with my energy
> > minimization. All I have done so far is to take the dppc128.pdb file and
> > the example2.top topology file from Peter Tieleman's site, run editconf and
> > grompp with en em.mdp file similar to John Kerrigan's tutorial, followed by
> > mdrun. Any help would be appreciated.
> My guess is the topology is broken, or doesn't correspond to the
> configuration. Get out VMD or something and look at things visually.
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Tsjerk A. Wassenaar, Ph.D.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
9747AG Groningen, The Netherlands
+31 50 363 4336
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