On 1/17/20 11:01 PM, Ashma Khan wrote:
Thank for your suggestion Alessandra I have applied the pbc conditions on my system in steps as follows: 1. gmx trjconv -f full_md.xtc -s full_md.tpr -pbc whole -o full_md_whole.xtc 2. gmx trjconv -f full_md_whole.xtc -s first_frame.gro -pbc nojump -o full_md_nojump.xtc 3. gmx trjconv -f full_md_nojump.xtc -s full_md.tpr -pbc mol -ur compact -center -o full_md_mol.xtc After applying all these conditions, peptides of dimer diffusing out of the box, both in opposite direction at the end of the simulation. kindly suggest me what should I do.
Center on one peptide only, to see if the other is re-wrapped in the central image along with it. If not, then you do not have a dimer at all times and the RMSD should be high. If they stay associated, re-calculate RMSD because the previous results were just a PBC artifact in that case. With any multimeric system, you cannot just center on "Protein" because the geometric center of the group can be exactly coincident with the center of the box with all the proteins at different faces/corners of the unit cell.
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