I am doing SMD of protein using NAMD with constant velocity pulling. In order to do the simulation, we have to specify the smd-atom (the atom to which the dummy atom is attached and then pulled). It is clearly given in the NAMD-tutorial. But, I want to pull a group of atoms, i.e., I need to get the centre of mass of the atoms and then attach the dummy atom to it. I am not sure how to add that in the input file where we give the force conditions and also mention the fixed atom.
Does anybody know how to do SMD with pulling a group of atoms instead of pulling a single atom using NAMD?
Hi,
You can create a group of atoms with a tcl script and then you can specify their center of mass. Then you could set a velocity (Group of atoms)that specified center of mass. You should set the tcl_forces on in NAMD conf file.
...
thanks Ali. but what will be the tcl script for setting the group of atoms and center of mass. suppose i want to pull 234 numbered amino acids in chain A and chain B both. and also set 234 numbered amino acid in chain C will be fixed. so can you give me the script ali.
Regards
- Badges
- Science topic