Hi,
somewhat off-topic but I wonder why in your free energy protocol you
only vary the vdW and electrostatic lambdas. What about the others?
Your mutation also transforms bonded terms and masses.
One minor point is that your duplication of atomtypes (with i and m
prefixes) seems pretty
Hi,
mdrun doesn't see any problems, but if something else is reporting 25%
utilization then that probably means you have something else running on
your machine, which is a terrible idea for running mdrun. You should expect
some slowdown wrt to the non-free-energy version of the run - the
somewhat off-topic but I wonder why in your free energy protocol you
only vary the vdW and electrostatic lambdas. What about the others?
Your mutation also transforms bonded terms and masses.
Minor point - if you are taking the difference between two mutations (say,
with and without a
On 5/19/15 12:12 PM, Hannes Loeffler wrote:
On Tue, 19 May 2015 12:03:41 -0400
Michael Shirts mrshi...@gmail.com wrote:
Yep, that's what I generally do. Almost all alchemical changes
involve a difference in two calculations (since the alchemical change
itself is unphysical). Even
On Tue, 19 May 2015 17:48:17 +0200
Julian Zachmann frankjulian.zachm...@uab.cat wrote:
Concerning the changes of the atom types: the changes in the charges
are really small and the results will probably be the same if I would
not convert the whole ligand, just the 4 atoms which are changing.
On Tue, 19 May 2015 11:37:11 -0400
Michael Shirts mrshi...@gmail.com wrote:
somewhat off-topic but I wonder why in your free energy protocol you
only vary the vdW and electrostatic lambdas. What about the others?
Your mutation also transforms bonded terms and masses.
Minor point -
Hello Hannes,
As Michael said it is better to leave most things untouched and just change
VDW and LJ - at least this is what I have been reading so far.
Concerning the changes of the atom types: the changes in the charges are
really small and the results will probably be the same if I would not
As Michael said it is better to leave most things untouched and just change
VDW and LJ - at least this is what I have been reading so far.
Well, I didn't quite say this. Changes in the bonded terms do not entirely
cancel. Changes in masses do 100% cancel because of the seperability of
Yep, that's what I generally do. Almost all alchemical changes involve a
difference in two calculations (since the alchemical change itself is
unphysical). Even one-calculation solvation free energy calculations are
actually calculating the difference in free energy from liquid to vapor
state.
Concerning the changes of the atom types: the changes in the charges
are really small and the results will probably be the same if I would
not convert the whole ligand, just the 4 atoms which are changing.
However, as i had both ligands parametrised, I thought it would be a
good idea to
On Tue, 19 May 2015 12:03:41 -0400
Michael Shirts mrshi...@gmail.com wrote:
Yep, that's what I generally do. Almost all alchemical changes
involve a difference in two calculations (since the alchemical change
itself is unphysical). Even one-calculation solvation free energy
calculations are
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