[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 13:32:29 CEST 2007
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: <chris.neale at utoronto.ca>
To: <gmx-users at 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" <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
>>>
>>> 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: <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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