[gmx-users] trjorder time-consuming

Rebeca García Fandiño regafan at hotmail.com
Wed Jun 3 14:52:37 CEST 2015


Dear GROMACS users,
I am using the command "gmx trjorder" with a single frame of a trajectory, to order the water molecules according to the smallest distance to a molecule. The system is very small (4400 atoms), however gmx trjorder is taking more than 1 hour to finish!! Is it normal to be so time-consuming using only a single frame or maybe is there anything wrong with the execution?

gmx trjorder -f frame.pdb -s topology.tpr -o frame_ordered.pdb -da 0 -na 3

Thanks a lot for your help in advance,

Rebeca

Dr. Rebeca García
Santiago de Compostela University
Spain
 		 	   		  


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