Most of the Literature i have seen with NAMD.is there any method or tools in Gromacs to study water and ion permeability of channels in gromacs? from trajectory or otherwise
NAMD and GROMACS are equivalent (both are molecular dynamics packages). If you can program the same system of NAMD in Gromacs, then you're all set.
VMD can read and analyse the obtained trajectory.
HI,
Fernando ,
Thanks, for your reply.I have 100ns Trajectory from Gromacs. Do you have any information how to calculate number of water molecules passing through channel per unit time ?
thanks
Can you show your structure? A snapshot image would be nice, including XYZ axes. Can you open it in VMD (easy analysis)?
Yeah..
You can see the channel in lipid bilayer which is blue and water box at each side. i added pore water too.
Nikhil: To find out "number of water molecules passing through channel per unit time", calculate (for every snapshot from the MD trajectory) the number of water molecules on each side of the lipid bilayer and in the channel. So, for each snapshot you will have three values: (1) water outside, (2) water in the channel, (3) water inside.
Subhomoi Borkotoky
, (1) define three containers (outside, channel, inside) using xyz coordinates, (2) assign each water molecule (defined by its xyz coordinates) to the container which contains the xyz coordinates of the water molecule, (3) count the water molecules in each container.- Badges
- Science topic