Hi Alex, Thank you for your reply. Here below is my response to your comments.
------------------------------------ hBN is hardly a common subject of simulation for Gromacs folks, but let's see... 1. When you run the simulation in vacuum, do you get the same error? Does a 300K vacuum simulation result in reasonable sheet behavior? What about NVT? ------------------------------------ The answer is yes. I ran more tests today, and I think I have found exactly how the error came out. In fact, if I remove the whole free energy calculation section from my mdp file, the system will run perfectly in parallel, both HBN in vacuum and HBN in solution. So I suspect somewhere in FEC section is causing the trouble. Then I looked up each command in GROMACS documentation, and found this "couple-intramol" flag: "couple-intramol: no All intra-molecular non-bonded interactions for moleculetype couple-moltype are replaced by exclusions and explicit pair interactions. In this manner the decoupled state of the molecule corresponds to the proper vacuum state without periodicity effects. yes The intra-molecular Van der Waals and Coulomb interactions are also turned on/off. This can be useful for partitioning free-energies of relatively large molecules, where the intra-molecular non-bonded interactions might lead to kinetically trapped vacuum conformations. The 1-4 pair interactions are not turned off." I wonder if the "couple-intramol = no" works periodic molecules. In my mdp file, I set the flag to "no", because both reference tutorials set it to "no". However, I am dealing with a relative large molecule with periodicity, so I should have set this flag to "yes". Then I ran several more test with "couple-intramol = yes". Now, for EM/NVT/NPT/PROD_MD, the system could finally run in parallel. No more disturbing errors. Hooray!! But I am still confused about the setting of "couple-intramol". Why it can run parallelly if "couple-intramol" is set "yes". The hBN sheet in my simulation is infinite with PBC. I wonder if the "couple-intramol = yes" is a must. Does it have any influence on the output results if we turn off the intra-molecular non-bonded interactions of a large infinite molecule? Please note that "periodic-molecules = yes" in all my simulations. ------------------------------------ 2. What GROMACS forcefield are you using and what are the nonbonded types for boron and nitrogen? ------------------------------------ There is no universal force field for HBN, so I am using a modified gromos54a7_atb force field, i.e., manually adding the parameters for boron and nitrogen to the bonded & nonbonded .itp files. The parameters are obtained from literature. ------------------------------------ 3. How was the topology obtained? If x2top was used, was the BN sample in a box with in-plane PBC? ------------------------------------ I did use x2top to generate the topology of hBN sheet by using the following command: g_x2top_mpi -f HBN-z-2.gro -o hbn-x2top.top -ff bnt_oplsaa -name BNT -noparam -pbc -alldih PBC is considered here. And some additional modifications are carried out manually. Best, Xuliang -- 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.