[gmx-users] strange movement

[Fan Gao]

Hi, all
I'm running a pentameric protein simluation by using Gromacs. I output the 
pdb files from the trajectory file and used VMD to visualize it. After 3ns 
simulation, 2 subunits of the protein suddenly move away from the other 3 
subunits (more than 10 angstom). Is there anyway to solve this problem? 
Should I use a larger water box?
Thanks,

Fan

Fan Gao

Receptor Biology Lab
Medical Science Building 1-145
Dept. of Physiology & Biomedical Engineering
Mayo Clinic, College of Medicine
Rochester, MN 55905
USA

Tel: 507-284-8461
Fax: 507-284-9420