[gmx-users] Removal of unwanted water from lipid bilayer after solvating the structure from genbox: problem and solution

Alok alokjain at iitk.ac.in
Sat Oct 27 08:22:17 CEST 2007

Dear Chris,

Thanks again for investing your valuable time on my problem.

I forgot to mention in my previous mail that, I have made total
two changes in the parameters. First I changed x/y compressibility from 0
(zero) to 4.5e-5 and second x/y ref_t from zero to 1.0 as you have

Pcoupl                       = Berendsen
 Pcoupltype               = semiisotropic
 tau_p                        =   2       2
 compressibility        =    0       4.5e-5
 ref_p                         =  0       1.0

Pcoupl                       = Berendsen
Pcoupltype                   = semiisotropic
tau_p                         =  2         2
compressibility              =  4.5e-5    4.5e-5
ref_p                        =  1.0       1.0

Mark suggestion came after seeing my original structure, actually the
original structure of pre-equilibrated POPE bilayer which I took from Dr.
Peter Tieleman web site, have a structure such that lipid molecules are
distributed irregularly , that's why after removing the unwanted water by
a script I was getting too much vacuum between water and head groups.

So mark suggested to take Z_max and Z_min manually after visual
inspection of bilayer, So I had supplied Z_max and Z_min manually to my
script (not calculated by my perl script after sorting the Z coordinates, as
I was doing previously). This way the extent of vacuum reduced a lot.

Later I had made changes in my parameter file as mentioned above (based on
your suggestion), till now after 1ns run, my structure looks fine to me.

Thanks a lot your and mark valuable suggestions and time.

PS: If moderator permit me then I will  post the picture (size 381
kb only) which will help to explain my problems and solution more clearly.

Best Regards,

----- Original Message ----- 
From: <chris.neale at utoronto.ca>
To: <gmx-users at gromacs.org>
Sent: Friday, October 26, 2007 10:19 PM
Subject: [gmx-users] solvate using genbox results in water in 
thecenterofthebilayer. How to edit pdb file contents in gromacs ?

> Dear Chris,
> I have ran the equilibration run till 225ps but water molecule are not 
> ready
> to stay at my desirable place :-( , I mean to say still I am getting 
> uneven
> distribution of water moleculers over lipid head groups. Even after 
> changing
> 0 to 4.5e-5.

I also suggested that you change ref_p to:
ref_p                        =  1.0       1.0

> PS: I have send a personal mail to Mark Abraham, because I have to send a
> picture to explain my problem, which gromacs mailing list does not permit.
> After that he gave me couples of suggetions. I have follow his suggetions
> along with incorporation of your suggetion (0 to 4.5e-5), till now it 
> looks
> like my problem is solved.

Could you please post all of the information to this site so that
others can benifit from it in the future plus those who assisted you
can understand what was going wrong?

Specifically, what are the old and new versions of the parameters that
you changed between when it didn't work and then when it did?

Also, if you make sure to include some keywords in your message then
it will be easy to search for.

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