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PIPS, e.g. PIP2 (POP2) and PIP3 (POP3), in insane
- andreashlarsen
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4 years 5 months ago #8324
by andreashlarsen
PIPS, e.g. PIP2 (POP2) and PIP3 (POP3), in insane was created by andreashlarsen
Hi,
I have had some issues with building bilayers with PIPs in insane - thought I would share it here for others encountering the same issues.
I used the version of insane that can be downloaded from the martini website (version not given in file).
First, insane did not automatically determine the charges (when running with the flag -salt 0). This could be changed by altering the following line in insane.py:
charges = {"ARG":1, "LYS":1, "ASP":-1, "GLU":-1, "DOPG":-1, "POPG":-1, "DOPS":-1, "POPS":-1, "DSSQ":-1, "POPI":-1, "POP1":-3, "POP2":-5, "POP3":-7}
Second, the bead names have been updated in the lipid itp files, but not in insane.py, giving warnings. The updated lines are:
"POPI": (moltype, " C1 C2 C3 PO4 - - - GL1 GL2 C1A D2A C3A C4A - - C1B C2B C3B C4B - - "),
"POP1": (moltype, " C1 C2 C3 PO4 P1 - - GL1 GL2 C1A D2A C3A C4A - - C1B C2B C3B C4B - - "),
"POP2": (moltype, " C1 C2 C3 PO4 P1 P2 - GL1 GL2 C1A D2A C3A C4A - - C1B C2B C3B C4B - - "),
"POP3": (moltype, " C1 C2 C3 PO4 P1 P2 P3 GL1 GL2 C1A D2A C3A C4A - - C1B C2B C3B C4B - - "),
of course one can also just ignore the errors, but I like better to run without them...
Thirdly, I had problems with my system blowing up under minimization and equilibration. I am doing simulations in Gromacs 2018. As stated clearly in the itp files (and described by Lopez et al 2013), one needs to add in the line:
define = -DFLEXIBLE
in the minimization mdp file and the equilibration mdp file. No blowing up after that...
let me know if something should have been done differently - and I hope the post is useful for someone out there.
Cheers,
Andreas
I have had some issues with building bilayers with PIPs in insane - thought I would share it here for others encountering the same issues.
I used the version of insane that can be downloaded from the martini website (version not given in file).
First, insane did not automatically determine the charges (when running with the flag -salt 0). This could be changed by altering the following line in insane.py:
charges = {"ARG":1, "LYS":1, "ASP":-1, "GLU":-1, "DOPG":-1, "POPG":-1, "DOPS":-1, "POPS":-1, "DSSQ":-1, "POPI":-1, "POP1":-3, "POP2":-5, "POP3":-7}
Second, the bead names have been updated in the lipid itp files, but not in insane.py, giving warnings. The updated lines are:
"POPI": (moltype, " C1 C2 C3 PO4 - - - GL1 GL2 C1A D2A C3A C4A - - C1B C2B C3B C4B - - "),
"POP1": (moltype, " C1 C2 C3 PO4 P1 - - GL1 GL2 C1A D2A C3A C4A - - C1B C2B C3B C4B - - "),
"POP2": (moltype, " C1 C2 C3 PO4 P1 P2 - GL1 GL2 C1A D2A C3A C4A - - C1B C2B C3B C4B - - "),
"POP3": (moltype, " C1 C2 C3 PO4 P1 P2 P3 GL1 GL2 C1A D2A C3A C4A - - C1B C2B C3B C4B - - "),
of course one can also just ignore the errors, but I like better to run without them...
Thirdly, I had problems with my system blowing up under minimization and equilibration. I am doing simulations in Gromacs 2018. As stated clearly in the itp files (and described by Lopez et al 2013), one needs to add in the line:
define = -DFLEXIBLE
in the minimization mdp file and the equilibration mdp file. No blowing up after that...
let me know if something should have been done differently - and I hope the post is useful for someone out there.
Cheers,
Andreas
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