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.

Ren Kong Ph.D.

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