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

chris.neale at utoronto.ca chris.neale at utoronto.ca
Thu Oct 25 07:07:42 CEST 2007

> 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.


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

to be changed to:

   if [ "$count" = 4 ]; then

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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