Hello everyone,
I am trying to calculate the number of hbond/water molecule and hbond lifetime by cpptraj in Ambertools17. I have a 22x22x22 ang^3 bulk water. I got the topology file in .mol2 file format and trajectory file in .dcd file format from LAMMPS. But when I ran those files in cpptraj I ran into two issues I can't solve. (1). The number of hbond/molecule is 1.27 whereas it should have been near 3.5. (2). I couldn't calculate the lifetime of hbond by runanalysis command. Here's what I did.
parm waterfinal.mol2 # My topology filetrajin hbond.dcd # My trajcetory file (100 frames)
hbond HB distance 3.5 angle 150 out hbvtime.dat avgout avhhb.dat # This gave me two filesrunrunanalysis lifetime HB out lifehb.dat
ACTION OUTPUT: 34884 solute-solute hydrogen bond Does it mean I have a total of 34884 bonds over 100 frames?Error says:Warning: 'HB' selects no data sets.
Error: No data sets selected.
Error: lifetime: Could not add data sets.
So, I can calculate the number of hbonds but not the lifetime.Can anyone point out the mistake in my approach?
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Received on Tue Aug 08 2017 - 13:30:02 PDT
