Re: [gmx-users] confusion on energy for a system of protein sovated in water

On 2/22/16 10:03 PM, Ming Tang wrote: Thanks Justin, How about LJ and Coulomb energy? I want to see the trend of protein energy only. I defined 2 energy group: protein and SOL in .mdp file. Then, I saw LJ and Coulomb: protein-ptrotein option when using g_energy. Are they VDW and Coulomb

Re: [gmx-users] confusion on energy for a system of protein sovated in water

Thanks Justin, How about LJ and Coulomb energy? I want to see the trend of protein energy only. I defined 2 energy group: protein and SOL in .mdp file. Then, I saw LJ and Coulomb: protein-ptrotein option when using g_energy. Are they VDW and Coulomb force within the protein only? --

Re: [gmx-users] confusion on energy for a system of protein sovated in water

On 2/22/16 8:33 PM, Ming Tang wrote: Dear lists, After pulling a protein in water and performing mdrun -rerun, I found that G96Bond, G96Angle, COM-Pull-En and Potential energy extracted from the original system using g_energy -f ener.edr , and from the -rerun system using g_energy -f

[gmx-users] confusion on energy for a system of protein sovated in water

Dear lists, After pulling a protein in water and performing mdrun -rerun, I found that G96Bond, G96Angle, COM-Pull-En and Potential energy extracted from the original system using g_energy -f ener.edr , and from the -rerun system using g_energy -f rerun.edr have different values. Firstly, are