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Questions about the MARTINI
- Jinyoung
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3 years 1 month ago #8879
by Jinyoung
Questions about the MARTINI was created by Jinyoung
Hi everyone!
Recently I'v tried to use MARTINI-ff in gromacs and had the equilibrated coarse-grained transmembrane Protein-POPC bilayer system with ~ 550000 atoms. After I implemented NVT/NPT equilibration step, I wanted to start pulling simulation in my CG transmembrane Protein-POPC bilayer system.
But I got many LINCS Warnings during the protein pulling simulation, and it makes the simulation aborted.
My questions is
1. I simulated the NPT equilibration for 0.02ps * 100000 times = 200 ps.
Is it not enough to make my system stabilized? (I checked the area per lipid)
2. If I need more equilibration, how can I set the time step, 2 fs or 20 fs with polarizable water?
3. As I know the LINCS warning comes from the clashed structure. How could I solve LINCS warnings. Could The 'GMX_MAXCONSTRWARN=-1' option can be used without problem?
Thank your for considering my question!
Recently I'v tried to use MARTINI-ff in gromacs and had the equilibrated coarse-grained transmembrane Protein-POPC bilayer system with ~ 550000 atoms. After I implemented NVT/NPT equilibration step, I wanted to start pulling simulation in my CG transmembrane Protein-POPC bilayer system.
But I got many LINCS Warnings during the protein pulling simulation, and it makes the simulation aborted.
My questions is
1. I simulated the NPT equilibration for 0.02ps * 100000 times = 200 ps.
Is it not enough to make my system stabilized? (I checked the area per lipid)
2. If I need more equilibration, how can I set the time step, 2 fs or 20 fs with polarizable water?
3. As I know the LINCS warning comes from the clashed structure. How could I solve LINCS warnings. Could The 'GMX_MAXCONSTRWARN=-1' option can be used without problem?
Thank your for considering my question!
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