Hi Mike,
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).
Best,
Tsjerk
On 10/19/06, Mark Abraham <[EMAIL PROTECTED]> 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.
Mark
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--
Tsjerk A. Wassenaar, Ph.D.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336
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