On Thu, May 24, 2012 at 5:24 PM, Turgay Cakmak <[email protected]>wrote:
> > 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 > Catenate two trajectory with help of trjcat -h to get snapshot of particular time use trjconv -dump <time> use appropriate pbc option you are using -b 10000 -e 10000 means the snapshot at 10 ns So I think conf20.gro is snapshot at 20 ns so they may differ ... With Best Wishes, Rama David
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