[gmx-users] Weird structure after minimization (membrane protein simulation)

[Mark Abraham]

Alok wrote:

> @Mark:
> Thanks a lot for your reply/comments and time. I am using TIP4P water 
> model, and I really could not understand why it happens, Some of the 
> bonds of the water molecules are broken down, and after 1ps MD  they 
> make bonds again. Is it not very strange?

No. Your visual representation "makes" bonds, not the simulation. The 
simulation can move the interatomic distances so that the heuristic no 
longer detects bonds, and this is what we're trying to diagnose.

> I have tried to visualize in 
> different visualization tool but still problem was persisting. I was not 
> able to implement your suggestion regarding tolerance limit of the 
> visualization software, I used rasmol, chimera, insightII but could not 
> found any such option. I am still trying for that, if I could found it, 
> I will inform you the result after that.  I am really worried about 
> temporary LINCE warning
> which I was getting. Is there any way to resolve this issue?

I endorse the suggestion Chris made here.

Mark