[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:
> 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,
> 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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