Hi all,
I’m running GROMACS to simulate a simple phospholipid bilayer membrane (POPC) under deformation, and plot the von Mises stress-strain curve to determine yielding point. I have got the membrane deformed and extractred output pressures from .edr file (option PRESS X, PRESS Y, PRESS Z) to calculate the stress, then use that calculated stress and true strain to plot the curve. The general shape of the curve is correct; however, the pressure value fluctuates widely in GROMACS and the yield stress/ yield strain is wrong. Why did I get the wrong value and where/ which parameter files should I address to solve this problem? 1. I got a lower yield stress and a higher yield strain than it should be (compared to previous research findings on similar problem using LAMMPS). Why did I get this problem, and what should I fix to get the right yielding stress/strain values? 2. Is the wrong value due to the incorrect bonding or constraint between the molecules? If this is the case, which files or which parameters should I look into to modify the bond or constraints? Does lower yield stress and higher yield strain means that the bond in GROMACS is more ductile? 3. Sometimes I run the same simulation several times without changing anything to double check. I can get similar results most of the time, but sometimes the simulation stop faster and an error is reported like this “The domain decomposition grid has shifted too much in the Z-direction around cell 0 0 3. This should not have happened. Running with fewer ranks might avoid this issue”. What does this error mean? What is domain decomposition? Is the Domain Decomposition automatically set in GROMACS for running simulation? Thank you very much for sharing your time. Sincerely, Anh Vo -- 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.