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.
No, there's no "extra bond". Your visualization software probably uses
some heuristic to decide whether to *render* a bond between two atoms...
it's certainly not using your .top file where you defined your bonds, or
the .tpr generated from it, since neither of these will now have an
extra bond. Does the structure actually look bad? Do the contents of
your .top file (and included .itp files) actually mean what you think
they mean?
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.
Read the output to pdb2gmx, editconf and genbox carefully.
Mark
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