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gmx sasa AND gmx energy
- Guruge
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2 years 10 hours ago - 2 years 9 hours ago #9380
by Guruge
gmx sasa AND gmx energy was created by Guruge
Dear MARTINI users,
I have a system with water and lipids. During the simulation, lipids are aggregated and I want to calculate the solvent-accessible surface area (SASA) for each lipid component and the potential energy of the system. I have the following two questions.
1) Can I use 'gmx energy' to calculate the potential energy? Do I have to consider a scaling factor?
2) How do I calculate SASA for different lipids using gmx sasa tool? How do I get vdwradii.dat file for CG beads?
Appreciate, if someone could help me.
Thank you.
I have a system with water and lipids. During the simulation, lipids are aggregated and I want to calculate the solvent-accessible surface area (SASA) for each lipid component and the potential energy of the system. I have the following two questions.
1) Can I use 'gmx energy' to calculate the potential energy? Do I have to consider a scaling factor?
2) How do I calculate SASA for different lipids using gmx sasa tool? How do I get vdwradii.dat file for CG beads?
Appreciate, if someone could help me.
Thank you.
Last edit: 2 years 9 hours ago by Guruge.
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