Dear gromacs users; I am trying to perform micelle clustering analysis as described in gromcas website:
1. use trjconv <http://www.gromacs.org/Documentation/Gromacs_Utilities/trjconv> -pbc cluster to obtain a single frame that has all of the lipids in the unit cell. This must be the first frame of your trajectory. A similar frame from some previous timepoint will not work. 2. use grompp <http://www.gromacs.org/Documentation/Gromacs_Utilities/grompp> to make a new tpr file based on the frame that was output from the step above. 3. use trjconv <http://www.gromacs.org/Documentation/Gromacs_Utilities/trjconv> -pbc nojump to produce the desired trajectory using the newly produced tpr file. Firstly I am trying to use trjconv to have a .gro file, but the output of first step gives me a .gro file in improper format, i.e.coordinates are not written with required spaces between each other. Here is my command line: gmx trjconv -f mytrajectory.xtc -o micelle.gro -s mytopology.tpr -e 0.001 -pbc cluster And here is the micelle.gro file: 1CHOA ROH 1 2.7 8.2 7.7 1CHOA R1 2 3.0 8.1 7.7 1CHOA R2 3 3.2 8.1 7.8 1CHOA RO2 4 3.2 7.8 7.7 1CHOA RO3 5 3.4 7.8 7.9 1CHOA R3 6 3.4 7.8 7.7 1CHOA C1 7 3.6 7.5 7.7 1CHOA OCO 8 3.5 7.1 7.6 What can be the possible reason for this error and how can I fix it? With regards, Esra -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.