[gmx-users] Membrane protein simulation

Yanzi Zhou yz30 at nyu.edu
Wed Dec 19 19:10:23 CET 2007

Dear Behnoush:
> Dear Yanzi,
> Forthunatly my simulation was run. this time I select the pope files of the Dr Tieleman's site and create the protein_in_pope.pdb with ffgmx force field.
> Then I ran genbox to solvate the system and delete some pope which had crash with the protein.Also I added #include "lipid.itp" in the last generated .top file and change the charactr of system at the end of the file based on the total number of protein.pope and water. So grompp has been run.
> But I have already two questions. After grompp, I ran genion to neutralize the system. But this run has not any output and it seems it has stopped in this step by these two lines in the end:
> Number of (3-atomic) solvent molecules: 6113
> Replacing solvent molecule 717 (atom 18791) with CL- 
It means that the system has 6113 solvent molecules and one of them is 
replaced by CL-. So you can find the coordinate file named out.gro, and 
if you have used the option  "-p topol.top", you will find your topolopy 
file has changed also.
> and there is no interaction. Could you please explain to me what it means and what I should do.
> Another problem is the protein size is greater than the box in the both sides. What is your suggestion to me for expanding the water size in both sides of the box?
What do you mean by both sides? If you mean the Z axis, you should 
expand the box and add more water, because we use period boundary 
conditions, the protein doesn't want to see itself. But be careful, POPE 
may not suitable for this protein. If you mean the X or Y axis, you 
should use a larger system of POPE, more lipids and more water.
> Thank you very much in advance for your very kind help.
> Best regards
> Behnoush
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Best Regards.

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