Dear Chris,
Thanks a lot your suggestions.
I have started the MD based on your suggestions. I will tell you as soon I
will get the results.
PS: Is this is already reported that Gromacs have some problem with ZERO?
Regards,
Alok
----- Original Message -----
From: <[EMAIL PROTECTED]>
To: <gmx-users@gromacs.org>
Sent: Thursday, October 25, 2007 1:47 PM
Subject: [gmx-users] solvate using genbox results in water in the
>centerofthe bilayer. How to edit pdb file contents in gromacs ?
Dear Chris,
Thanks for your time and suggestion.
I tried all the possible pressure couplings (including semiisotropic) and
run it for around 500ps.Gap between head group and water molecule
disappear,
but I was getting uneven distribution of water molecules. I am pasting my
previous mail again. Hope I will get any solution for my problem.
Best Regards,
Alok
##############################################################
Dear Mark,
Thanks a lot for your valuable time, and sorry for inappropriate
description, I am describing again, I hope thin time I can make it clear.
I took preequilibrated POPE.pdb files which already have SPC water
molecules
I had deleted these water molecules and change the box size at 'Z Axis'
only, so I can accommodate more water, then using genbox I had added TIP4P
water molecules, but it also added the water molecules in the interior of
the bilayer. So I deleted these water by the criteria if the 'Z'
coordinate
of the water in between the 'Z_min' and 'Z_max' of 'C13' (where branching
of
the POPE molecules start) atom. After that I got the files which don't
have
any water at the interior of the bilayer but there is a vaccuum between
lipid head group and TIP4P water molecules (I defined it as a ZONE in my
previous mail). As discussed in the mailing list so many times I can do
same
thing by increasing the VdW radius of lipid atoms. But after that I was
expecting these vacuum will be vanished and water molecules will spread
homogenously after sort span of MD, as suggested in the mailing list. But
here problem has started I run MD till 500ps, but water molecules are
clustered at some places, at some places there is no water or very less
water. i.e. I am getting uneven distribution of water molecules over lipid
head groups.
So I thought this problem might be due to pressure coupling or type of
ensemble I am using (might be I am wrong here !).
I ran four different sort MD by using isotropic, semiisotropic,
anisotropic
pressure coupling and last one no pressure coupling (NVT ensemble). But in
all the cases I am getting similar structure at last which is uneven
distribution of TIP4P water molecules over head groups.
The parameters I used for diffrent couplings all mentioned below.
Isotropic: (First Simulation)
diffrent = Berendsen
Pcoupltype = isotropic
tau_p = 2.0
compressibility = 4.5e-5
ref_p = 1
semiisotroic: (Second Simulation)
Pcoupl = Berendsen
Pcoupltype = semiisotropic
tau_p = 2 2
compressibility = 0 4.5e-5
ref_p = 0 1.0
What's going on here? Apparently x/y stays the same and Z can scale? I
am relatively sure that this is your problem. try this:
semiisotroic: (Second Simulation)
Pcoupl = Berendsen
Pcoupltype = semiisotropic
tau_p = 2 2
compressibility = 4.5e-5 4.5e-5
ref_p = 1.0 1.0
**Note that I personally use tau_p=4 but 2 should be fine also.
Also note that there may _possibly_ be some issue with gromacs that
makes the zeroes not work as they should, but I would rather suspect
that everything is working as it should and that it is just not
working as you might expect. Try the above suggestion and let me know
hoe it works out.
Chris.
anisotropic: (Third Simulation)
Pcoupl = Berendsen
pcoupltype = anisotropic
tau_p = 10.0 10.0 10.0 0
0
compressibility = 4.5e-5 4.5e-5 4.5e-5 0 0
0
ref_p = 1.0 1.0 1.0 0
0 0
I would avoid anisotropic. In any event, still I would avoid zeroes.
NVT (Fourth Simulation).
I hope I make my problem clear.could some one give some idea what
parameters/ensemble I should take to overcome this problem. please
suggest
me where I am doing mistake.
Thanks
Regards,
Alok
----- Original Message -----
From: "Mark Abraham" <[EMAIL PROTECTED]>
To: "Discussion list for GROMACS users" <gmx-users@gromacs.org>
Sent: Friday, October 19, 2007 11:58 AM
Subject: Re: [gmx-users] uneven distribution of water across the bilayer
Alok wrote:
Dear All,
I am trying to simulate lipid-water system (340 POPE lipids & 6120
TIP4P
Waters), during the solvation by genbox, It also add the the water at
the
interior of the bilayer. I removed those water molecules by my perl
script. But after removing these water molecules I have observed a zone
between the lipid head group and water.
You'll have to describe that "zone" better if you want us to understand
what you're talking about. Read genbox -h where it mentions vdwradii.dat
I tried to do small simulations (50 to250 ps) using different pressure
coupling but still I am not getting the structure which have homogeneous
arrangement of water over lipid head group. There is uneven distribution
of water across the bilayer.
Are these last two observations related, or not?
During this sort simulations position restrain on lipid was applied.
Check your waters aren't restrained too.
I tried Isotropic, semiisotropic,anisotropic pressure coupling with the
following parameter, but no luck
I think you need to read section 7.3.14 of the manual. You're using
combinations of parameter values that don't make sense.
Isotropic:
Pcoupl = Berendsen
Pcoupltype = isotropic
tau_p = 2.0
compressibility = 4.5e-5
ref_p = 1
semiisotropic:
Pcoupl = Berendsen
Pcoupltype = semiisotropic
tau_p = 2 2
compressibility = 0 4.5e-5
ref_p = 0 1.0
anisotropic:
Pcoupl = Berendsen
pcoupltype = anisotropic
tau_p = 10.0 10.0 10.0 0 0
compressibility = 4.5e-5 4.5e-5 4.5e-5 0 0 0
ref_p = 1.0 1.0 1.0 0 0
I also tried NVT Ensemble but no success till now.
So the problem is something other than the way you're setting up your
ensemble.
could some one give
some idea what parameters I should take to overcome this problem. I
searched the mailing list this problem discussed so many time suggestion
was after sort simulation (10-20 ps) water will arrange properly,but I
am
not able to get proper arrangement of water molecules. please suggest me
where I am doing mistake.
Other parameters od the MDP file.
define = -DPOSRES_LIPID
integrator = md
dt = 0.002
nsteps = 25000
nstcomm = 1
nstxout = 1000
nstvout = 500
nstlog = 100
nstenergy = 100
nstxtcout = 500
xtc_precision = 1000
xtc_grps = POPE SOL
energygrps = POPE SOL
nstlist = 10
ns_type = grid
pbc = xyz
rlist = 0.9
coulombtype = PME
rcoulomb = 0.9
rvdw = 1.2
fourierspacing = 0.12
pme_order = 6
ewald_rtol = 1e-5
optimize_fft = yes
vdw-type = Cut-off
gen_vel = yes
gen_temp = 300
gen_seed = 173529
constraints = all-bonds
constraint_algorithm = lincs
unconstrained_start = no
lincs_order = 4
lincs_iter = 1
lincs_warnangle = 30
That looks OK at a glance.
Mark
----- Original Message -----
From: <[EMAIL PROTECTED]>
To: <gmx-users@gromacs.org>
Sent: Thursday, October 25, 2007 10:37 AM
Subject: [gmx-users] solvate using genbox results in water in the
centerofthe bilayer. How to edit pdb file contents in gromacs ?
You can do it by two different methods.
1) You can increase the default VdW radii of the lipid atoms in
/usr/local/
gromacs/share/top/vdwradii.dat file (path might be different from your
system), say 0.5 for carbon, so genbox will not add the water inside the
bilayer.
Cleaner method is to:
cp /usr/local/gromacs/share/top/vdwradii.dat ./vdwradii.dat
and then modify the local file.
but you will find a gap between lipid head groups and water molecules
which can be resolved after some ps dynamics. (I personally have not yet
got the success ;-) )
Do I understand you to say that for you the gap does not completely
dissapear in <500ps? Did you use semiisotropic coupling? Otherwise it
will be more difficult for this space to fill in. It should fill in
really quite quickly (<<500ps)... has for me.
2) You can write a small script which can delete these water molecules,
I
wrote a script for the same if you need contact me offline.
I have previously posted such a script. It takes 10-30 minutes to run
since it's not sophisticated, but it does work very well.
http://www.gromacs.org/pipermail/gmx-users/2006-May/021526.html
I forgot to mention that in the previously referenced script there is
an assumption that you use a 3 atom water molecule. If you use tip4p
then you would want
if [ "$count" = 3 ]; then
count=0
fi
to be changed to:
if [ "$count" = 4 ]; then
count=0
fi
and etc for tip5p.
Hope it will help
Alok
----- Original Message -----
Hi
I am using editconf to try to add water layers on either side of my
bilayer. I use the following command:
genbox -cp popc.gro -box 12.47820 12.35940 10.0 -o solvated.gro -cs
spc216.gro -p topology.top
However, because the center of the bilayer region is less dense, a lot
of water molecules are created inside the bilayer.
- How does one usually edit pdb files in gromacs, in terms of, for
example, removing water molecules from the center of a bilayer ?
Thank you
-Maria
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