Re: [gmx-users] mdrun -rerun problems
George Abadir wrote: Hi all, I am running simulations of carbon nanotubes and amino acids in water. I need to calculate the potential energies for the whole system as well as the interaction energy between the CNT and amino acid. What I am tried to do is to calculate the energy for the whole system first (i.e. I did not introduce any energygrps in the run.mdp file) and then use the rerun option to calculate the interaction energy after introducing energygrps= CNT Protein SOL into the run.mdp file. However, each time I try to run this second step the cluster on which I run the simulation crashes with a message Kernel panicked! Does any body know about this problem? Yeah, something's broken that's probably got nothing to do with GROMACS, or the fact you're doing a re-run. Is there another way to get both the potential energy of the system as well as the interaction potential energy? I understand that if I write energygrps= CNT Protein SOL from the very beginning the energy of the whole system won't be written, is that right? mdrun always calculates the total potential and kinetic energy, and outputs it according to nstxxx flags. Have you not looked at typical output, or typical .edr file contents? Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] mdrun -rerun problems
Yes of course I looked at the output but I thought is I specify energy groups it will output only those specified and not the whole system. However I tried a short run and it did output both. For the crash it turned out it is because all the nodes try to read the huge trajectory file at the same time if this may help somebody in the future. We are still trying to figure out how to solve this problem anyway. Thanks for your time. George Mark Abraham wrote: George Abadir wrote: Hi all, I am running simulations of carbon nanotubes and amino acids in water. I need to calculate the potential energies for the whole system as well as the interaction energy between the CNT and amino acid. What I am tried to do is to calculate the energy for the whole system first (i.e. I did not introduce any energygrps in the run.mdp file) and then use the rerun option to calculate the interaction energy after introducing energygrps= CNT Protein SOL into the run.mdp file. However, each time I try to run this second step the cluster on which I run the simulation crashes with a message Kernel panicked! Does any body know about this problem? Yeah, something's broken that's probably got nothing to do with GROMACS, or the fact you're doing a re-run. Is there another way to get both the potential energy of the system as well as the interaction potential energy? I understand that if I write energygrps= CNT Protein SOL from the very beginning the energy of the whole system won't be written, is that right? mdrun always calculates the total potential and kinetic energy, and outputs it according to nstxxx flags. Have you not looked at typical output, or typical .edr file contents? Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
