For an additive force field, the two numbers are in agreement, E_tot -
E_13 - E_23 - E_33 = E_12, by definition. You can easily design a test
case that will prove this.
I know. I have it in front of me. ;)
The dielectric constant of the medium is not included in the
calculation, at least not
On 4/11/18 3:09 PM, Alex wrote:
Mark, Justin:
This is two against one, even though noone was questioning the
additivity of energy in forcefields with constant charges, etc.
So, let's go back specifically to solvation. Consider a system with
two oppositely charged ions (1 and 2) in water of
Mark, Justin:
This is two against one, even though noone was questioning the
additivity of energy in forcefields with constant charges, etc.
So, let's go back specifically to solvation. Consider a system with two
oppositely charged ions (1 and 2) in water of your choosing (group 3).
For extr
Hi,
What Justin said, plus the observation that you should know how you plan to
analyze the results before you run the simulation. In this case, that means
knowing what you'll learn from rerun energies. Sometimes this means that
you won't ever run the simulations, and those are the really efficien
On 4/11/18 4:21 AM, Alex wrote:
Screening effects in Gromacs come in a rather non-straightforward
manner in terms of data extraction: they certainly exist within the
simulations in the form of the fields induced by local water
orientation, but to extract them from reruns is extremely challeng
BS”D
Ok, thanks for the advice,
Harry
On 11 Apr 2018, at 11:21 AM, Alex
mailto:nedoma...@gmail.com>> wrote:
Screening effects in Gromacs come in a rather non-straightforward manner in
terms of data extraction: they certainly exist within the simulations in the
form of the fields induced by
Screening effects in Gromacs come in a rather non-straightforward manner
in terms of data extraction: they certainly exist within the simulations
in the form of the fields induced by local water orientation, but to
extract them from reruns is extremely challenging even if you're
outputting wate
BS”D
Dear Alex,
Not *explicitly* related to water: we would like to look at interaction
energies between parts of proteins, or proteins and DNA. So screening comes to
mind…
Harry
On 11 Apr 2018, at 10:51 AM, Alex
mailto:nedoma...@gmail.com>> wrote:
If you plan to extract anything exp
If you plan to extract anything explicitly related to water from your
reruns -- very much so. Basically unusable trajectories.
Alex
On 4/11/2018 1:48 AM, Harry Mark Greenblatt wrote:
B”SD
In an effort to reduce the size of output xtc files of simulations of large
systems, we thought of savi