[gmx-users] water molecules

Mark Abraham Mark.Abraham at anu.edu.au
Fri Jun 16 03:54:17 CEST 2006

Beniamino Sciacca wrote:
> Dear GMX users,
> Viewing my simulations  with VMD I see water molecules that become 
> longer; in fact in the simulation I can see some lines (that are water 
> molecules).
> Why?
> Is that a simulation problem or a VMD one?

I can't tell from your description. Unless you use trjconv properly, VMD 
will show water molecules that cross the simulation cell boundaries with 
lines joining atoms on opposite sides of the simulation cell. If "become 
longer" means only a gradual and incremental increase, then you have a 
simulation problem.


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