[gmx-users] solvate using genbox results in water in the centerofthe bilayer. How to edit pdb file contents in gromacs ?
Alok
alokjain at iitk.ac.in
Thu Oct 25 08:27:13 CEST 2007
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
anisotropic: (Third Simulation)
Pcoupl = Berendsen
pcoupltype = anisotropic
tau_p = 10.0 10.0 10.0 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
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" <Mark.Abraham at anu.edu.au>
To: "Discussion list for GROMACS users" <gmx-users at 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
>> 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 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: <chris.neale at utoronto.ca>
To: <gmx-users at 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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