On 10/29/19 4:44 AM, Olga Press wrote:
Prof. Lemkul thank you for your replay.
I was inaccurate with my question, what I mean is: why does the "bubble"
phenomenon does not occur during the NVT equilibration in a system where
the protein is embedded inside a *membrane*? (I observed this
Prof. Lemkul thank you for your replay.
I was inaccurate with my question, what I mean is: why does the "bubble"
phenomenon does not occur during the NVT equilibration in a system where
the protein is embedded inside a *membrane*? (I observed this phenomenon
only when the protein is on the
On 10/28/19 3:27 AM, Olga Press wrote:
Prof. Justin thanks so much for the explanation.
Why this phenomenon was not observed during the NVT equilibration when I
run a simulation of embedded protein?
A protein alone in water is surrounded by an isotropic medium that does
not exhibit the same
Prof. Justin thanks so much for the explanation.
Why this phenomenon was not observed during the NVT equilibration when I
run a simulation of embedded protein?
Do two equilibrations of NPT assemble, first with position restraint on the
protein (50ns) and second without restains (about 200ns) will
On 10/27/19 1:20 PM, Olga Press wrote:
Prof. Justin thank you for replay.
The leaflets are not simply separating, the membrane is deformed and
resembles a "chromosome".
The image is in the following URL:
Prof. Justin thank you for replay.
The leaflets are not simply separating, the membrane is deformed and
resembles a "chromosome".
The image is in the following URL:
On 10/27/19 11:10 AM, Olga Press wrote:
Dear Gromacs users,
I run 10ns NVT equilibration with position restains (on the protein) for a
system in which the protein is on the membrane surface.
I used the following .mdp file
title = NVT equilibration for p1-DOPC
define =
Dear Gromacs users,
I run 10ns NVT equilibration with position restains (on the protein) for a
system in which the protein is on the membrane surface.
I used the following .mdp file
title = NVT equilibration for p1-DOPC
define = -DPOSRES ; position restrain the protein
;
