I am trying a coarse-grained simulation in gromacs to understand certain protein folding. I initially tried with triclinic box and -d 1.0. I used -c to center my protein in the solvent box. But the protein moved out of the solvent box during the simulation.
I tried a second time in a cubic box and -d 2.0. It didn't help.
Any suggestions in this regard?
Thanks
Try to use gmx trjconv -f file.trr - n index.ndx -pcb whole, this should maintain the structure of the molecule in box.
if the result is not as expected, replace the whole option by nojump
GMX trjconv: http://manual.gromacs.org/programs/gmx-trjconv.html
see if this could help:
https://pdfs.semanticscholar.org/31e3/a23cda3e880a08025e3f1becb168b7b9097d.pdf
I feel that you have checked your protein structure after production run by using ngmx option or u may loaded your xtc and tpr file vmd?
First of all,
remove the water molecules from your system by making index file by using gmx make_ndx command
generate a new trajectory file by using trjconv command like
gmx trjconv -f file.xtc -s file.tpr -n index.ndx -o new.xtc -fit rot+trans or -pbc nojump
than this traj file you can check in ngmx as well as by extracting the structures in few intervals and visualize them.
it might be helpful
Good Luck
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