Hi Gromacs users, I have a problem getting a snapshots using trjconv. If you could help me, I would be very grateful. Below, I try to explain what I did and problem happened. Firstly, I have done 10ns long simulation (several peptides in a box). And then, using the outputs of that simulation (conf10ns.gro and 10ns.cpt files), I extend the simulation 10 ns more and I get conf20ns.gro, trj20ns.xtc,….
Then I used the following to get snapshot of the last frame. trjconv –f traj20ns.xtc –s topol.tpr –b 10000 –e 10000 –o snapshot20ns.gro (Note: traj20ns.xtc is not a full trajectory, it just a trajectory of second 10ns simulation) When I looked these two files (conf20ns.gro and snapshot20ns.gro) at the VMD, they were completely different configurations. As far as I know, the last frame is written in conf20ns.gro. So they must be the same. What is wrong here? By the way, I defined dt=0,002, nstxout=1000 and nsteps=5000000 in my mdp file. Thanks in advance, Turgay
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