Hi again,
I thought your suggestions would work for my membrane, but it seems like the
removal of COM translation of the bilayer and water separately does not stop
the system from translating in the box. My new simulations are now soon
crashing again since the lipids are crossing the pbc. I was
Hi again,
I thought your suggestions would work for my membrane, but it seems like the
removal of COM translation of the bilayer and water separately does not stop
the system from translating in the box. My new simulations are now soon
crashing again since the lipids are crossing the pbc. I was
Do you have sufficient water on either side of your membrane? That is, are
the lipids crossing PBC because of spurious interactions with the other side of
the membrane? That would certainly be a reason for a crash - the model physics
is breaking down. How did you generate your initial
It is indeed not clear how you system may translate still! Is this
translation on
the z axis? How much does it move and how quick?
On Apr 29, 2010, at 3:09 PM, Justin A. Lemkul wrote:
Do you have sufficient water on either side of your membrane?
That is, are the lipids crossing PBC
My system consists of 128 lipids and 3655 water molecules and is one of the
structures one can download from University of Calgary. I think that the water
phase is thick enough because when I run non-constrained simulations and the
system translates there is no crash when the lipids cross the
ERIKSSON, EMMA wrote:
My system consists of 128 lipids and 3655 water molecules and is one of the
structures one can download from University of Calgary. I think that the water
phase is thick enough because when I run non-constrained simulations and the
system translates there is no crash
The last section of my mdp file:
pull = constraint
pull_geometry= cylinder
pull_r1 = 1.0
pull_r0 = 1.5
pull_group0 = DPPC
pull_group1 = MOL
pull_vec1= 0 0 1
pull_init1 = 3.083
The translation occurs in the z direction, yes. I'm running many constrained
simulations but in general the movement of the new simulations, in which the
COM translation has been removed for the bilayer and water separately, is about
1 nm in 3 ns. The movement is slower than when I was running
ERIKSSON, EMMA wrote:
The last section of my mdp file:
pull = constraint pull_geometry= cylinder
pull_r1 = 1.0 pull_r0 = 1.5 pull_group0
= DPPC pull_group1 = MOL pull_vec1= 0 0 1
pull_init1
The increase in z box length is due to that I have replaced 12 DPPC lipids by
cholesterol molecules. Cholesterol reduces the area per lipid and compresses
the bilayer lateral (xy) area, resulting in a slight increase in the water
layer thickness. I have performed exactly the same simulations
ERIKSSON, EMMA wrote:
The increase in z box length is due to that I have replaced 12 DPPC lipids by
cholesterol molecules. Cholesterol reduces the area per lipid and compresses
the bilayer lateral (xy) area, resulting in a slight increase in the water
layer thickness. I have performed exactly
Well 1 nm / 3 ns is definitely not reasonable! That is about 1 m /
s ... 3.6 km/h
We has seen motion of the COM of a bilayer using CG models but the
motions
were ~ 0.1 nm on the mircosecond timescale! This is due to the way COM
is
removed ... not exact but appears only on large time
Justin, you understood it correctly; I only have problems with the low
cholesterol concentration.
According to g_traj -com the COM of DPPC in one of the simulations moves 0.6 nm
in 3.5 ns. And as Xavier just wrote it's quite much...
My mdp file looks like this:
title=
ERIKSSON, EMMA wrote:
Pcoupl = Parrinello-Rahman
pcoupltype = semiisotropic
tau_p= 1.0 1.0e-14
compressibility = 4.5e-5 4.5e-15
I would bet almost anything that this is the cause of your problem. How did you
come up with these
ERIKSSON, EMMA wrote:
I was using those strange values of tau_p and compressibility to keep the z
box length fixed in order to avoid problems associated with scaling the
positions of the molecules in the box when we constrain the distance between
DPPC and the small molecule. I was told to use
Justin A. Lemkul wrote:
ERIKSSON, EMMA wrote:
I was using those strange values of tau_p and compressibility to
keep the z
box length fixed in order to avoid problems associated with scaling the
positions of the molecules in the box when we constrain the distance
between
DPPC and the small
The crash seems to be expected as by crossing the pbc the distance
will change significantly
and in way the algorithm can not handle.
Note that the overall translational motion of your system should
always be removed.
The removal of the COM motion of your bilayer should be sufficient to
Hi again,
Thanks Xavier for your reply. I didn't know that this mdp option existed.
However, I read the manual and also checked the mdout.mdp files for my previous
simulations, and I understood it as if those are the default settings even if
you don't specify any of them in the md.mdp file. The
ERIKSSON, EMMA wrote:
Hi again,
Thanks Xavier for your reply. I didn't know that this mdp option
existed. However, I read the manual and also checked the mdout.mdp files
for my previous simulations, and I understood it as if those are the
default settings even if you don't specify any of
you should remove the water and lipid bilayer COM separately.
I am not sure what you should do with your small molecule though.
Probably best to add it to the bilayer as you constrain their relative
position!
On Apr 27, 2010, at 4:32 PM, ERIKSSON, EMMA wrote:
Hi again,
Thanks Xavier for your
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