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, Mark Abraham wrote:
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 w
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 time, but
> I need the VdW i
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 correct
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 not I turn off all the non-
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 t
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 wr
Hello,
I am running simulations of two protein domains in tip4p water and 0.15M
salt concentration that contain up to 650,000 atoms total. The protein
domains are separated from each other at the start of each simulation and I
am measuring how the distance between them changes over time.
Now, I n