hello
I want to simulate gold nanoparticles with proteins. I've made a PDF file
containing the nanoparticles and proteins, using Hayprkm software.then Ihave
used thisPDF fileto start the simulation by gromacs. But in the early stage of
equilibrium, I am faced with the following error.
application called MPI_Abort(MPI_COMM_WORLD, -1) - procesee 17application
called MPI_Abort (MPI_COMM_WORLD, -1) - process Source code file:pme.c, line:538
Fatal error:
2 particles communicated to PME node 17 are more than 2/3 times the cut-off out
of the domain decomposition cell of the This usually means that your system is
not well equilibrated.
I've read previous questions and it is said that the system is unstable, but
how do I equilibrium the system?
I'm having this trouble in equilibrium step Before beginning of MD.
I equilibrate my system in 5 steps. by 5 em.mdp file that I named them em1.mdp,
em2.mdp,em3.mdp, md100.mdp(temperature=100 k),md200.mdp(temperature=200k) and
after these steps I do main simulation in 300k. I attached all mdp file.
in md100.mdp steps, mdrun stops in middle of running and appear above error.
please help me to resolve my problem
thank you
Fatemeh Ramezani
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
