[gmx-users] Expanded ensemble error

Dear Gromacs users, I wanted to use expanded ensemble for calculating solvation free energy of a drug molecule in the water based on "Ethanol solvation with expanded ensemble in gromacs". in this example the integrator, t coupl, pcoupl, and constraint-algorithm were set to md-vv, Nose-Hoover,

[gmx-users] Jump of drug to other side of lipid bilayer

Dear,I have done a simulation of DMPC lipid bilayer for 50 ns which has 10 drug molecules which were positioned in the water phase in the beginning of simulation. In the first 10 ns of simulation, one of the drug molecules diffuses from water into the other side of lipid bilayer and remains

[gmx-users] Jumping to other side of box

Dear Users, I have done a simulation of DMPC lipid bilayer which has 10 drug molecules in the water phase for 50 ns. In the first 10 ns of simulation, one of the drug molecules diffuses from water into the other side of lipid bilayer and remains there. I applied (trjconv –pbc mol), (trjconv

[gmx-users] Free energy calculation for aminoacids

Hi all I want to calculate free energy of solvation for a leucine and some other aminoacids individually,according to Justin tutorial : methane in the water. Is it reasonable to follow that method for free energy determination of one amino acid? Cheers -- Gromacs Users mailing list *

[gmx-users] Free energy calculation for aminoacids

Hi all I want to calculate free energy of solvation for a leucine and some other aminoacids individually,according to Justin tutorial : methane in the water. Is it reasonable to follow that method for free energy determination of one amino acid? Cheers body {height: 100%; color:#00;

[gmx-users] angle distribution between a vector and Z axis

Dears, I simulated a DMPC lipid bilayer. I want to calculate the distribution of angle between phosphorus - nitrogen vector (P-N vector) and Z axis. Is there any command to calculate angle distribution between a vector and an axis? My Gromacs version is 4.5.4. I searched and found gangle

[gmx-users] angle distribution between a vector and Z axis

Dears, I simulated a DMPC lipid bilayer. I want to calculate the distribution of angle between phosphorus - nitrogen vector (P-N vector) and Z axis. Is there any command to calculate angle distribution between a vector and an axis? My Gromacs version is 4.5.4. I searched and found

[gmx-users] angle distribution between a vector and Z axis

Dears, I simulated a DMPC lipid bilayer. I want to calculate the distribution of angle between phosphorus - nitrogen vector (P-N vector) and Z axis. Is there any command to calculate angle distribution between a vector and an axis? My Gromacs version is 4.5.4. I searched and found