[gmx-users] Re: something wrong about making hole...

Senthil Kandasamy senthilk at engin.umich.edu
Fri Feb 21 18:44:09 CET 2003

Hi Xianhui,

I have been making a lot of holes using the md-run hole program (Thanks 
again to Graham Smith).
As Erik said, the most likely reason for your problems is badly clashing 
atoms when you insert the protein.
The first thing you should probably check is the gsurf.log file 
generated by the hole-mdrun program.
Especially, check the third column (distance of the deepest atom from 
If there are to many atoms left inside your cylinder or if the deepest 
atom is very deep in your hole,
 then you will not be able to energy minimized once you merge the 
protein with the bilayer.
You might have to run the mdrun-hole program for longer times.
You can also try using really large values for the normal force (500 or 
even 1000) to drive out most of the atoms.
 But this might badly distort some of the lipids and might need a fairly 
lengthy equilibaration run after insertion, but is still worth trying.
Hope this was helpful


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