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 would use normal MD with distance restraints between suitable terminal
atoms. This is a much simpler approach to this problem.
I keep getting the following error during the
simulation:
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
See http://wiki.gromacs.org/index.php/blowing_up
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?
That's not your problem. Atoms 5 and 10 are too close because there's
something unphysical about your model, and anyway these atoms are not
your terminal pair.
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.
There are a few links here
http://wiki.gromacs.org/index.php/Coordinate_File that might help.
Mark
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