From: Benedetta Sampoli Benitez (
Date: Wed Jan 27 2021 - 11:44:46 CST


I have run 100 ns simulations in NAMD of a ternary complex of a protein/DNA/incoming nucleotide, but the protein gets out of the water box during the simulation. In addition, the DNA and incoming nucleotide also “jump” in and out of the water box. I have tried to recenter using PBC wrap. This seems to fix the DNA and incoming nucleotide “jumping”, but the water box gets squashed. Is there a way to maintain the octahedral water box?

Thank you,

Benedetta Sampoli Benitez, Ph.D. | Chair, Division of the Sciences
Professor of Chemistry and Biochemistry
Pre-Health Advisor<>
(212) 517-0563
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