Dear Gromacs Users, I run md simulation of protein in water obtaining trajectory. Because in VMD my protein was jumping plus I had some part of my protein shaded in some frames I could not catch one place to create a movie I used:
trjconv -f md.trr -s md.tpr -pbc nojump -o mdnojump.xtc trjconv -f mdnojump.xtc -s md.tpr -center -o mdfinal.xtc Now, I have still the same problem - it jumps on my screen but not as much as previously. Can you suggest what can I do to find one place in order to make a movie observing conformational changes? Steven
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