VMD-L Mailing List

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

Hello,

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,
Biba

[signature_302268551]
Benedetta Sampoli Benitez, Ph.D. | Chair, Division of the Sciences
Professor of Chemistry and Biochemistry
Pre-Health Advisor
bsampoli_at_mmm.edu<mailto:bsampoli_at_mmm.edu>
(212) 517-0563
221 East 71st Street, New York, NY 10021


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