From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Wed Jul 27 2011 - 12:49:24 CDT
Dear all,
To save computational time I would normally set the integration parameters
to something like:
timestep 2; #fs
rigidBonds all
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 20
longSplitting C2
cutoff 12.
switching on
switchdist 10.
pairlistdist 14
Now I'm doing some ABF simulations in the membrane. Since
ABF already infinitely helps with the sampling along my colvars, would it
make sense to switch to more expensive but precise integrator parameters?
timestep 1; #fs
rigidBonds water
nonbondedFreq 1
fullElectFrequency 1
I realize that all the degrees of freedom not in included the colvars are
not better sampled (for example the lipid tails) so perhaps it's still
better to go with the 2 fs time step...
But on the other hand, the forces introduced by ABF might get quite large so
a smaller timestep would insure a more stable simulation.
Thank you for your advice and experience,
Best regards,
Ajasja Ljubetic,
Young researcher
Laboratory of biophysics
Department F5
Institute Jozef Stefan
Ljubljana, Slovenia
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