Ashutosh Jogalekar wrote:
Well, the log file says that the protocol is dying even before it
starts the MD...so it stops right after it says
'Initializing LINear Constraint Solver'
after which it displays the segmentation fault.
OK, LINCS is an algorithm that constrains bond lengths - either
explicitly in your solute, or implicitly in (lots of) solvents. If it's
crashing there, then gromacs is very confused about your topology for
some reason. If this is the phenylglycine peptide, go back and fix that
before worrying about why this is happening.
More than likely the weird residue numbering is also symptomatic of
having incorrectly specified your modified residue. I think you should
work on that first.
There should be no need to parameterize acetyl - it's in the OPLS AA
.rtp file as a separate residue.
Mark
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