Re: [gmx-users] regarding umbrella sampling

thank you for your reply. because without the position restraint the cylindrical shape of my molecule (CNT) changes. is it reasonble to use umbrella sampling along with the position restraint in y and z directions? - Original Message - From: Justin Lemkul To: Abed Askari

[gmx-users] regarding umbrella sampling

Dear gmx-users I want to use umbrella sampling to calculate the PMF between two molecules and x-axis is the reaction coordinate. would you please tell me I can use position restraint in y and z directions for the pulling group or not?  any help would be appreciated. -- gmx-users mailing list

[gmx-users] regarding US

ear gmx-users I want to use umbrella sampling to calculate the PMF between two molecules and x-axis is the reaction coordinate. would you please tell me I can use position restraint in y and z directions for the pulling group or not?  any help would be appreciated. -- gmx-users mailing list

[gmx-users] orientation of CNT

Dear gmx users I would like to simulate a system: carbon nanotube+some small molecules. first I want to align CNT along the z direction. to do that I used the commands: editconf -f cnt.pdb -o cnt.gro -princ -box 5 5  5 editconf -f cnt.gro -o nano.gro  -rotate 0 90 0 and then I used genbox: genbox

[gmx-users] place carbon nanotube along the z direction

Dear gmx-users I would like to orient my carbon nanotube along the z direction. would you please tell me how I can do that?Do I use any option other than -box when I use editconf or something?my command was editconf -f cnt.pdb -o cnt.gro -box 5   5   5 any help would be really appreciated. Best reg