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From: Hélder Bandarra Tavares (H.D.BandarraTavares_at_tudelft.nl)
Date: Mon Jun 01 2020 - 11:00:09 CDT

I want to determine the length of a molecule in 0.3 M KCl and I was wondering if it would be feasible with NAMD. I minimized/equilibrated it after solvation under the right conditions but the resulting conformation is very similar to the initial one, with almost the same length, so I'm not sure what to conclude from that.

I also ran a production simulation and got multiple conformations, but I'm not sure what to conclude from that either. Would the production frame with the lowest energy give me the right conformation and length?

I appreciate any help/thoughts on this.

Hélder Tavares