VMD-L Mailing List

From: Yuan Xue (yuan.xue_at_biu.ac.il)
Date: Sat Mar 02 2024 - 10:42:54 CST

After running “pbc wrap -all -centersel “protein” -center com -compound residue”, all the water molecules all of a sudden cling to the protein on the last frame, even though they appear scattered in the box in all previous frames. This repeatedly occurred for every section throughout the trajectory, which was evenly sliced into 20 sections to ease uploading to VMD.
Is there a way to make sure water molecules are correctly represented throughout the trajectory?

[https://urldefense.com/v3/__https://res.cdn.office.net/assets/mail/file-icon/png/photo_16x16.png*vmd-shots.png__;XQ!!DZ3fjg!95_6Htxrk0DBHENGXka3QvO_P4WPc3-MUxgtx4bQMhpxjJzsibOSsOWQfKYxoezf19q-NZuo7vgqdLlV9-iP$ <https://urldefense.com/v3/__https://biu365-my.sharepoint.com/:i:/g/personal/xueyuan_biu_ac_il/EcCCiJ3dT8lEt7_O15rYjoUB82sk-2VMl5LJp7ZjyvqB1w__;!!DZ3fjg!95_6Htxrk0DBHENGXka3QvO_P4WPc3-MUxgtx4bQMhpxjJzsibOSsOWQfKYxoezf19q-NZuo7vgqdNStHFjh$ >

Ava Yuan Xue

PhD Candidate at the Senderowitz Lab

Bar-Ilan University