[gmx-users] Urea molecule deformed in urea-water simulations using ffamber99

[George Abadir]

Hi,
     I am doing a simple simulation of one urea molecule dissolved in 
water. I am using the ffamber_urea.itp introduced in the AMBER port for 
GROMACS. I build a box using editconf and solvate the urea molecule 
using genbox with the fftip3p.itp water model also included with the 
AMBER port. After energy minimization (which converges to machine 
precision but not to the desired emtol=100. Actually the maximum force 
is about 550 for a cubic box), I find that there is one extra bond in 
the urea molecule between the oxygen atom and the nitrogen atom N1 and 
this bond was not there prior to energy minimization.
I gave it a shot with the production simulation after that, but sure 
enough, it gave a segmentation fault (I am not surprised with that 
because of the bad energy minimization).
Can anyone help me know why the energy minimization fails and the urea 
molecule becomes deformed? Your help is much appreciated.
Thank you very much,
Regards,
George B. Abadir