[gmx-users] calculation of angle between two groups

2012-07-26 Thread niaz poorgholami
Dear gmx users I did the simulations of carbon nanotube+surfactant+water molecules and I would like to calculate probability distribution of the angle formed between the vector of the surfactant molecules and CNT. Is there any tools or programs in gromacs to do that?I have tried g_sgangle program

Re: [gmx-users] calculation of angle between two groups

2012-07-26 Thread Mark Abraham
On 26/07/2012 8:21 PM, niaz poorgholami wrote: Dear gmx users I did the simulations of carbon nanotube+surfactant+water molecules and I would like to calculate probability distribution of the angle formed between the vector of the surfactant molecules and CNT. Is there any tools or programs in

[gmx-users] calculation of angle between two groups

2012-07-26 Thread niaz poorgholami
Dear Mark thank you for your concern.when I tried the g_sgangle program it gave me Fatal error: Something wrong with contents of index file. the index file was the one I used during the simulation and I made that with this command: make_ndx -f em.gro -o index.ndx and the groups for temperature

Re: [gmx-users] calculation of angle between two groups

2012-07-26 Thread Justin Lemkul
On 7/26/12 9:48 AM, niaz poorgholami wrote: Dear Mark thank you for your concern.when I tried the g_sgangle program it gave me Fatal error: Something wrong with contents of index file. the index file was the one I used during the simulation and I made that with this command: make_ndx -f em.gro