[gmx-users] Box Exploding Error
Justin A. Lemkul
jalemkul at vt.edu
Sun Jan 11 00:44:54 CET 2009
VENKATESH HARIHARAN wrote:
> Hello All,
> First, for this question I am referring to GROMACS 3.3.3. I have
> thoroughly read the archives for errors on why a simulation box might
> explode. My simulations require that I bring the N and C terminal ends
> of a ~20 amino acid peptide as close together as possible. To do this,
> I am using the pull code to freeze the C terminus and pull the N
> Terminus toward it. I keep getting the following error during the
> Back Off! I just backed up md_traj.xtc to ./#md_traj.xtc.1#
> Warning: 1-4 interaction between 5 and 10 at distance 1.480 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
> My question: Is there any way to completely ignore this error, so that
> the N Terminus is pulled as close as possible to the C Terminus? I
> understand that the results in the .pdo file of the pull simulation may
> be unrealistic, but I simply need to get a peptide structure whose N and
> C Terminal ends are close together (within .5 nm). On a side note, are
> there any suggestions for respectable molecular modeling software with
> which I may be able to BUILD a circular peptide (i.e. - N and C Terminal
> ends are brought close together)? Any help is appreciated.
This type of error should not be ignored. It means there is something
physically unrealistic about your system. Either you are pulling too fast or
somehow incorrectly, or the parameters you are otherwise using are incompatible
with the procedure.
Have you considered using distance restraints instead?
> Venkatesh Hariharan
> The Pennsylvania State University
> Schreyer Honors College
> Undergraduate - Bioengineering
> "You must be the change you wish to see in the world."
> --Mohandas Karamchand Gandhi
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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