Dear Gromacs users I am trying to simulate peptide in 30% TFE/water complex. Using parallel processing, I ran this system for 100ns using 2 nodes. The peptide is known to obtain helical conformation in this system. After 100ns, the peptide was found to be 37% helical. I ran the same system again on 1 node instead of 2, with no changes in the parameter or the input files. After 100ns of the simulation, the peptide was found to be 44% helical. Why is there so much change in the results? Which of the two should be considered?
The following commands were used: Simulation run on 1 node: mpirun -np 12 -hostfile host /share/apps/gromacs/bin/mdrun_mpi -v -deffnm peptide Simulation run on 2 nodes: mpirun -np 24 -hostfile host /share/apps/gromacs/bin/mdrun_mpi -v -deffnm peptide Kindly help. -- Sanket B Ghawali Junior Research Fellow ICMR-Biomedical Informatics Centre National Institute for Research in Reproductive Health Parel, Mumbai. -- 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.
