[gmx-users] bug in mdrun::::anomaly in final structure

[Shuaib Shahid]

Hi,

I am running simulations with two layers of charged atoms at the center of a box of water.  The layers are centered and seperated by 4 layers of a second type of uncharged atom. all are position restrained.  When i mdrun my simulation my final structure has all the charged atoms towards one side and the uncharged ones on the other side.  

However when i load my initial structure and the trajectory file then the last frame works fine and the atoms do not behave as they do in confout.gro

does anyone else get this?

thanks

Shuaib Shahid
University of Glasgow
Glasgow, Scotland
www.gla.ac.uk