FW: water layer in membrane protein modeling

From: Kong, Ren (rkong_at_tmhs.org)
Date: Thu Jul 18 2013 - 09:24:06 CDT

Hi all,

I'm a new user for membrane protein in water with NAMD. I have run a 100 ns simulation and found that the upper/lower water layer changed a lot compared with the initial structure. The thickness of upper water layer decreased a lot while the lower one increased.
The TIP3P explicit water model is used and the system is in a rectangle box. WrapWater and wrapAll are set to on to wrap the water and other molecules to central cell.

My questions are:

1. Can I consider the change of water layer as the effect of periodic condition?

2. Can I use this structure to run the simulation continuously (I want to prolong the simulation time)? Or should I retain only the protein and membrane and re-solvate the system?

3. I found that the residue ID of water, like 289, occurred several times in the last snapshot I extracted. That means in the one structure file (for example, snapshot from 100 ns), I can identify seven "water 289". Is this make sense?

Thank you so much for your help.

Best,
Ren Kong Ph.D.

Houston Methodist. Leading Medicine. Ranked by U.S.News & World Report as one of America's "Best Hospitals" in 12 specialties. Named to FORTUNE® Magazine's "100 Best Companies to Work For®" list eight years in a row. Designated as a Magnet hospital for excellence in nursing. Visit us at houstonmethodist.org. Follow us at twitter.com/MethodistHosp and facebook.com/HoustonMethodist. ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.

This archive was generated by hypermail 2.1.6 : Tue Dec 31 2013 - 23:23:29 CST