I suspect that you need to re-equilibrate your box volume to the new
solute parameters -- the volume probably needs to increase. Run a
simulation with a much smaller timestep and the Berendsen barostat and
the SD integrator. If this is stable, then use the output coordinates
of that to start your simulation with your desired parameters.
-- original message --
Hi,
I have scaled the non-bonded parameters(charges and epsilon) of tip3p atoms
in ffnonbonded.itp file(charmm forcefield). They are scaled by a ratio of
3/5. The simulation is then run at 500K for the protein water system. The
temperature exploded after first 20 steps. This does not happen if I run the
simulations with the unscaled parameters. I have also tried this with T=400
and temperature remains stable.
Pooja
--
Quaerendo Invenietis-Seek and you shall discover.
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