VMD-L Mailing List

From: Yuan Xue (yuan.xue_at_biu.ac.il)
Date: Wed Mar 06 2024 - 20:47:01 CST

The system (860,000+ atoms) contains only water molecules and a protein. The command was "pbc wrap -all -centersel "protein" -center com -compound residue."
Later to speed up wrapping qwrap was used instead (sel "not protein" center protein). In both cases, however, abnormal bonds still persisted after wrapping (picture attached).

Also, as I'm calculating the number of water molecules inside a region of the protein channel, the numbers vary significantly between the same frame in the trajectory, depending on the way of slicing the trajectory. For example, the last 50ns of a trajectory from 0-250ns don't match the first 50ns of a trajectory sliced from 200-500, although both overlap from 200-250ns. Specifically, towards the end of a sliced trajectory, water molecules tend to condense around protein (either visually so or not) and cause much higher number of counts.

Could anybody shed some light on any of these issues?

[https://urldefense.com/v3/__https://res.cdn.office.net/assets/mail/file-icon/png/photo_16x16.png*after-wrapping.png__;XQ!!DZ3fjg!-fgeiodCHmixK496zw1DxzBNp-sGsGvScDIQ4eP9knJyGsrTpet5Y4D-Xoay7GCchKRpKLjGFHmhSFx5cOB0$ <https://urldefense.com/v3/__https://biu365-my.sharepoint.com/:i:/g/personal/xueyuan_biu_ac_il/EY_LLGvfpFZPuj5zC6KL4ewBZcSq1uBa0AxMGziy6WRZtA__;!!DZ3fjg!-fgeiodCHmixK496zw1DxzBNp-sGsGvScDIQ4eP9knJyGsrTpet5Y4D-Xoay7GCchKRpKLjGFHmhSOaSwvxz$ >

Ava Yuan Xue

PhD Candidate at the Senderowitz Lab

Bar-Ilan University