Restraints to maintain shape of particle

From: Raman Preet Singh (
Date: Tue Mar 08 2022 - 05:24:47 CST

Dear All,

I am performing unbiased MD to study interactions of a metal cluster (hundreds of metal atoms without any interatomic bonds) with proteins. I would like that the spherical shape of the clustered atoms remains intact during interactions as observed in our experiments. I have tried position restraints to fix the position of atoms in the metal cluster while keeping the protein unrestrained but this does not lead to expected interactions. Hence, I would like that the metal cluster exist as a free floating sphere in TIP3P water but without loosing its characteristic shape. In other words, the relative positions of atoms “within the cluster” should remain fixed while the cluster, as a whole, moves in the solvent (and interacts with the protein). Is there a way to do this?


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