Re: [gmx-users] Conceptual question about the representation of dihedral angles in Gromacs

2012-10-27 Thread Arman Mahboubi Soufiani
Dear Andrew, I am a beginner! However, I would like to record my interpretation of the concept you're confused about and evaluate it by what experts will comment later. I am pretty sure your first calculation of 2,7 kcal/mol is correct, however, since ethane is symmetrical molecule you don't need

Re: [gmx-users] Conceptual question about the representation of dihedral angles in Gromacs

2012-10-27 Thread David van der Spoel
On 2012-10-27 03:02, Andrew DeYoung wrote: Hi, If you have time, may I ask a conceptual question about how dihedral angles are specified in force fields? Consider ethane, a two-carbon hydrocarbon (H_3C-CH_3). It has two carbon atoms and six hydrogen atoms. Call the carbons C1 and C2. Hydroge

[gmx-users] Conceptual question about the representation of dihedral angles in Gromacs

2012-10-26 Thread Andrew DeYoung
Hi, If you have time, may I ask a conceptual question about how dihedral angles are specified in force fields? Consider ethane, a two-carbon hydrocarbon (H_3C-CH_3). It has two carbon atoms and six hydrogen atoms. Call the carbons C1 and C2. Hydrogens H1, H2, and H3 are bonded to C1. Hydrogen