ewald_rtol affects PME.
http://comments.gmane.org/gmane.science.biology.gromacs.user/50202
On Fri, Nov 14, 2014 at 10:39 AM, Johnny Lu wrote:
> In another mdp file, i specified "vdw-modifier=Potential-shift-Verlet",
> and then in the log file, I see the same line "vdw-modifier =
> Potential-shi
In another mdp file, i specified "vdw-modifier=Potential-shift-Verlet", and
then in the log file, I see the same line "vdw-modifier = Potential-shift",
and I use "cutoff-scheme = Verlet" in all of my simulations.
Since i use rlist=1.3, and verlet-buffer-drift=-1. I guess the line
"vdw-modifier=Pot
On Fri, Nov 14, 2014 at 3:51 PM, Johnny Lu wrote:
> I guess I get the idea now. F = -dV(x)/dx. So no time derivative is
> involved. So shifting the potential would not cause a suddenly impulse on
> the system.
>
> By the way, is Potential-shift the default vdw and coulomb-modifier (so
> that is u
I guess I get the idea now. F = -dV(x)/dx. So no time derivative is
involved. So shifting the potential would not cause a suddenly impulse on
the system.
By the way, is Potential-shift the default vdw and coulomb-modifier (so
that is used even if i didn't specify a modifier) for gromacs 4.6.7?
I d
Hi,
Try it and see ;-)
mdrun -nsteps 10 -reprod -deffnm shifted
mdrun -nsteps 10 -reprod -deffnm not-shifted
gmx check -f shifted -f2 not-shifted
gmx check -e shifted -e2 not-shifted
Alternatively, given that the forces are not computed from the energies
(e.g. by central difference or some such)
Hi.
If I change my potential from non-shifted to shift, will the sudden change
of energy from non-shifted to shifted potential at step 0 completely mess
up the equilibration?
Thanks again.
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