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.
________________________________________________________________________
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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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