Ali Ghamartale

2 Questions 13 Answers 0 Followers

Questions related from Ali Ghamartale

Is the any way to use clustsize keyword based on the center of mass in gromacs? or a specific atom?

I want to measure the number of monomers, dimer, ... between the same molecule in my simulation box. I am using the following code: gmx clustsize -f mdrunps.xtc -s mdrun.tpr -n index.ndx -tu ps -b...

12 December 2019 4,637 4 View

How can I measure the cluster size between center of mass?

I need to measure the aggregation of a type of molecule. The aggregation will happen if the COM of molecules becomes less than 0.85 nm. I think I should use g_clustsize but it normally calculates...

12 December 2019 2,286 4 View