[gmx-users] Long bond streches during simulations

Seera Suryanarayana palusoori at gmail.com
Wed Oct 29 11:21:05 CET 2014

Dear gromacs users

I have done mdrun upto 50ns by using the command "gmx mdrun -deffnm md_0_1
-nt 7.
I have total 8 threads  and I used 7 out of it along with graphic card
nvidia tesla 2075.

I first thing I would like to know that when I load the .trr or .xtc file
after the .gro file into the vmd  some bonds stretched very long are being
appeared parallel and vertical in red and white color. My question here is
"Appearing  long bond stretches  while loading into vmd right or wrong?"

At the end of the simulation my protein moves towards the side of the box.
After some time (frame no. 1564)  few residues moves away from protein and
some bonds stretched very long being appeared between that residues and
rest of protein.

Then the bond stretches  disappear from the frame number 1900 and again the
bond stretch  being appeared during  rest of the simulation and at the end
I got the final trajectory with some long bond stretching between some
residues those moved away from the protein and the rest of the protein.

Kindly inform me what could be the reason for the long bond stretching?

Thanks in advance
Graduate student

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