hi all, I was trying to analyze some h_bond interaction for a protein with one ligand. I tried two runs for the same one for 5 nsec and another for 10 nsec. What I found here is that, the h-bonds present in the 5 nsec trajectory are more than that in 10 nsec trajectory, h-bonds in 10 nsec run should be at least equal to that in 5 nsec run.
for the two trajectory i have taken out the 10 frames. are the interaction picked up by g_hbond are dependent on the full trajectory or the frames only. whether the two different run on the same input file with same parameter can be related or compared ? Can anybody help me in the same case by giving some explanation or giving right way to do it ? With Thanks, VIVEk
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