Hi all,
Is there any software or webserver to read the molecular dynamics (MD) simulation trajectory which obtained from Ab initio MD simulation to calculate the atom-atom radial distribution function (RDF).
Thanks in advance.
As the RDF is related to the probability of distances between particles, I assume you have not one but many complexes.
I do not know about ready made software but as the RDF is a slightly odd but simple quantity I think it is quite instructive to code it yourself. In my experience this helps considerably in interpreting the result
As successive snapshots will be correlated for a time that is difficult to estimate a priori I would generally resist the temptation to use multiple snapshots from the same simulation and concentrate on a single snapshot from a system with sufficiently many particles.
VMD is a freely available software to calculate RDF and many more properties.
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