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

David van der Spoel spoel at xray.bmc.uu.se
Thu Jun 14 22:38:20 CEST 2007

George Abadir wrote:
> 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
check the topology and compare with chapter 5 in the manual.

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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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