Re: [gmx-users] affect of water removal on subsequent energy calculations

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

Re: [gmx-users] affect of water removal on subsequent energy calculations

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

Re: [gmx-users] affect of water removal on subsequent energy calculations

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

Re: [gmx-users] affect of water removal on subsequent energy calculations

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

Re: [gmx-users] affect of water removal on subsequent energy calculations

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

Re: [gmx-users] affect of water removal on subsequent energy calculations

BS”D Ok, thanks for the advice, Harry On 11 Apr 2018, at 11:21 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

Re: [gmx-users] affect of water removal on subsequent energy calculations

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

Re: [gmx-users] affect of water removal on subsequent energy calculations

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 > wrote: If you plan

Re: [gmx-users] affect of water removal on subsequent energy calculations

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