[gmx-users] solvate using genbox results in water in thecenterofthe bilayer. How to edit pdb file contents in gromacs ?

[chris.neale at utoronto.ca]

> 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.