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

chris.neale at utoronto.ca chris.neale at utoronto.ca
Thu Oct 25 23:03:11 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.

ok, great.

> PS: Is this is already reported that Gromacs have some problem with ZERO?

No. And I don't believe that gromacs has a problem here. But it is  
something that you could test. For example... is the z changing at all  
in your simulation? I only mentioned anything about it because I have  
no personal knowledge that it works correctly with zeroes from my own  
experience. That of course doesn't make it incorrect :) but I would  
prefer for you to try using some set of conditions that I do know  
personally to work correctly.

> Regards,
> Alok

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