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 differences (anisotropy) in forces that are
inherent to membranes.
Do two equilibrations of NPT assemble, first with position restraint on the
protein (50ns) and second without restains (about 200ns) will be sufficient
to fix the problem?
You should be able to resolve the bubble faster than that.
-Justin
Thanks a lot
Olga
בתאריך יום א׳, 27 באוק׳ 2019 ב-20:45 מאת Justin Lemkul <jalem...@vt.edu
>:
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:
https://spaces.hightail.com/space/8l6z0Tncyv/files/fi-f3882907-6f37-4230-8c12-40b1f7b1ef22/fv-41ef812d-a030-412f-890f-677af406ebe6/on%20DOPC.JPG
The protein is on the DOPC surface, that's why I'm not sure about the
setting of the .mdp file. I used the same .mdp settings for
the membrae-protein system, where the protein is embedded in a membrane.
I would be very grateful if you can help me with that.
What you're observing is exactly what I was talking about. It's a bubble
in the membrane, leading to the separation of the leaflets. This comes
from in adequate water to fill the volume of the unit cell; the waters
(which diffuse much faster than the lipids) rush to fill void space and
equilibrate their density, but since the ensemble is NVT, the box cannot
change size, leaving voids where the waters were. The lipids expand to
fill the voids (the polar head groups are drawn to the waters more
strongly than the lipid tails are held together) and you get a bubble.
Continuing with a sufficiently long NPT relaxation will fix this.
-Justin
Best regards,
Olga
בתאריך יום א׳, 27 באוק׳ 2019 ב-18:04 מאת Justin Lemkul <
jalem...@vt.edu
>:
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 = -DPOSRES ; position restrain the protein
; Run parameters
integrator = md ; leap-frog integrator
nsteps = 5000000 ; 0.002ps * 5000000 = 10000
ps=10ns
dt = 0.002 ; 2 fs
; OUTPUT CONTROL OPTIONS
; Output frequency for coords (x), velocities (v) and forces (f)
nstxout = 0
nstvout = 0
nstfout = 0
; Output frequency for energies to log file and energy file
nstlog = 10000
nstcalcenergy = 100
nstenergy = 1000
; Output frequency and precision for .xtc file
nstxout-compressed = 10000
compressed-x-precision = 1000
; This selects the subset of atoms for the compressed
; trajectory file. You can select multiple groups. By
; default, all atoms will be written.
compressed-x-grps =
; Selection of energy groups
energygrps =
; Bond parameters
continuation = no ; first dynamics run
constraint_algorithm = lincs ; holonomic constraints
constraints = h-bonds ; H bonds constrained
fit
to charmm36 ff
lincs_iter = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
ns_type = grid ; search neighboring grid cels
nstlist = 5 ; 10 fs
cutoff-scheme = Verlet
vdwtype = cutoff
vdw-modifier = force-switch ; same as vfswitch
rvdw-switch = 1.0
rlist = 1.2 ; short-range neighborlist cutoff (in
nm)
rcoulomb = 1.2 ; short-range electrostatic cutoff (in
nm)
; Electrostatics
coulombtype = PME ; Particle Mesh Ewald for long-range
electrostatics
pme_order = 4 ; cubic interpolation
fourierspacing = 0.12 ; grid spacing for FFT
; Temperature coupling is on
tcoupl = V-rescale ; modified Berendsen
thermostat
*tc-grps = Protein DOPC SOL_SOD_CLA* ; three coupling
groups -
more accurate
tau_t = 0.1 0.1 0.1 ; time constant, in ps
ref_t = 310.15 310.15 310.15 ; reference
temperature,
one for each group, in K
; Pressure coupling is off
pcoupl = no ; no pressure coupling in NVT
; Periodic boundary conditions
pbc = xyz ; 3-D PBC
; Dispersion correction
DispCorr = no ; Do not apply dispertion correction for
bilayers
by using charmm36 ff
; Velocity generation
gen_vel = yes ; assign velocities from Maxwell
distribution
gen_temp = 310.15 ; temperature for Maxwell
distribution
gen_seed = -1 ; generate a random seed
; COM motion removal
; These options remove motion of the protein/bilayer relative to the
solvent/ions
nstcomm = 100
comm-mode = Linear
*comm-grps = Protein_DOPC SOL_SOD_CLA*
However, the membrane seems to be breaking apart, the image of the
system
is attached to the mail.
The mailing list does not accept attachments. If you wish to share a
file or an image, upload it to a file-sharing service and provide a URL.
If the leaflets are simply separating, this is normal during NVT and
will resolve when running NPT.
-Justin
I think that it is the issue of the center-of-mass motion removal, but
I'm
not sure and would be very grateful for any suggestions.
Best regards,
Olga
--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall
Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com
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==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall
Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com
==================================================
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posting!
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send a mail to gmx-users-requ...@gromacs.org.
--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall
Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com
==================================================
--
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http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
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