Re: FW: water layer in membrane protein modeling

From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Thu Jul 18 2013 - 10:00:19 CDT

> **
>
> **1. **Can I consider the change of water layer as the effect of
> periodic condition?
>
Yes, your membrane is drifting upwards (so the waters at the top get
wrapped around). You can restrain the membrane COM using the colvars
module, but I don't think this is worth the trouble (and the possible
performance hit).

> ****
>
> **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?
>
Most probably. Resolvating would make no sense as you would have to
equilibrate a bit and so forth.

> ****
>
> **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? ****
>
> **
>
Do you have several different segments of water? In different segments the
resID can be repeated.

Regards,
Ajasja

This archive was generated by hypermail 2.1.6 : Wed Dec 31 2014 - 23:21:26 CST