Re: [gmx-users] Calculation of the Force on the center of bonds

2013-02-11 Thread Rasoul Nasiri
Dear Erik, Many thanks for your comment. The situation seems to be similar to TIP4P water model where the M site is located among the three other atoms. In my case, it's between the two C-H atoms. Could I ask you which parameters must be selected for these virtual sites? The interest molecule i

Re: [gmx-users] Calculation of the Force on the center of bonds

2013-02-11 Thread Erik Marklund
Try virtual sites constructions. On Feb 11, 2013, at 6:01 PM, Rasoul Nasiri wrote: Dear All, I need to define interaction sites on the center of C-H bonds instead of nuclei of each atom. The main reason was that non-bonding parameters (sigma and epsilon) have been parametrized in these centers

[gmx-users] Calculation of the Force on the center of bonds

2013-02-11 Thread Rasoul Nasiri
Dear All, I need to define interaction sites on the center of C-H bonds instead of nuclei of each atom. The main reason was that non-bonding parameters (sigma and epsilon) have been parametrized in these centers and those are only available for the center of C-H. So, I just wanted to know how ca