Re: [gmx-users] Turning off electrostatics between protein and water, then protein and protein

Hi, You can't decompose the "turning off" in the FE code by groups. You can turn off the coulomb in the protein, but that turns off its interactions with itself, solvent, and anything else Mark On Sun, Nov 19, 2017 at 9:27 PM Justin Lemkul wrote: > > > On 11/19/17 3:42 PM,

Re: [gmx-users] Turning off electrostatics between protein and water, then protein and protein

On 11/19/17 3:42 PM, Mark Abraham wrote: Hi, Oh, I see. Yes that feature turns off both kinds of non-bonded interactions. Then there is nothing useful for what you want. Couldn't this be done with the free energy code? Turn off protein-water electrostatics by running in the lambda=1 state

Re: [gmx-users] Turning off electrostatics between protein and water, then protein and protein

Hi, Oh, I see. Yes that feature turns off both kinds of non-bonded interactions. Then there is nothing useful for what you want. Mark On Sun, Nov 19, 2017 at 8:32 PM Aram Davtyan wrote: > Hi Mark, > > I apologize if I did not describe my problem correctly the first

Re: [gmx-users] Turning off electrostatics between protein and water, then protein and protein

Hi Mark, I apologize if I did not describe my problem correctly the first time, but I need the VdW interactions to stay on between all atoms at all times. I only need to turn off the electrostatic interactions between water and proteins. Thanks, Aram Hi, > > You've described the feature

Re: [gmx-users] Turning off electrostatics between protein and water, then protein and protein

Hi, You've described the feature correctly. Whether it is useful in a study design is another matter :-) Mark On Sun, Nov 19, 2017 at 8:00 PM Aram Davtyan wrote: > Hi Mark, > > I am not sure I understood. If I for example say "energygrp-excl = Protein > Water" would

Re: [gmx-users] Turning off electrostatics between protein and water, then protein and protein

Hi Mark, I am not sure I understood. If I for example say "energygrp-excl = Protein Water" would not I turn off all the non-bonded interactions between water and protein? Or did you mean something else? Thanks, Aram > Hi, > > In the group scheme you can turn on energy-group exclusions to get

Re: [gmx-users] Turning off electrostatics between protein and water, then protein and protein

Hi, In the group scheme you can turn on energy-group exclusions to get this working, but of course all of those states are sampling unphysical things from a broken forcefield. That can be OK, but you will have to be able to defend that claim. Mark On Sun, Nov 19, 2017 at 6:49 AM Aram Davtyan