[gmx-users] gold-protein simulation stop by error in equilibrum step
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 listgmx-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
Re: [gmx-users] gold-protein simulation stop by error in equilibrum step
On 12/6/12 3:12 PM, fatemeh ramezani wrote: 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 note that the mailing list does not accept attachments. The failure is either due to an incorrect topology, inadequate minimization, or unstable .mdp settings. Please also consult: http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-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
Re: [gmx-users] gold-protein simulation stop by error in equilibrum step
Am 06.12.2012 21:16, schrieb Justin Lemkul: On 12/6/12 3:12 PM, fatemeh ramezani wrote: 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. advertisement Concerning topologies and parameters: you can take a look at some of my and my collaborator's work: M. Hoefling, F. Iori, *S. Corni*, K.E. Gottschalk. Interaction of Amino Acids with the Au(111) Surface: Adsorption Free Energies from Molecular Dynamics Simulations, Langmuir 26, 8347 (2010) and F. Iori, R. Di Felice, E. Molinari, *S. Corni*, GolP: an atomistic force-field to describe the interaction of proteins with Au(111) surfaces , J. Comput. Chem., 1465 (2009). Best Martin -- gmx-users mailing listgmx-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
