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
Simulation run on 2 nodes:
mpirun -np 24 -hostfile host /share/apps/gromacs/bin/mdrun_mpi -v -deffnm
Sanket B Ghawali
Junior Research Fellow
ICMR-Biomedical Informatics Centre
National Institute for Research in Reproductive Health
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.