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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