Dear Gmx Users, I have compared average number of hbonds per time frame between my ligand and protein:
1) Using trajectory obtained straight after simulations: g_hbond -f md2.trr -s md2.tpr -n SystemGRP.ndx -num 91withLigandsHbond.xvg Avergage number of hbonds: 0.146 2) Using trajectory modified by trjconv according to the PBC workflow on www.gromcacs.org : g_hbond -f md2final2.xtc -s md2.tpr -n SystemGRP.ndx -num 91withLigandsHbond.xvg Avergage number of hbonds: 0.156 Does anyone know why this value changed and I obtained slightly different results? Thank you, Steven
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