Hello gmx-users! Sorry that I am bothering you all the time with energy conservation issues but this time I have problems with a crystal surface consisting of infinite polymer chains.
I think that simulation and interaction parameters employed should be conserving the total energy: time step of 0.5fs, PME with a slab correction for Coulombic interactions (f-spacing=0.1, pme-order=6, ewald-rtol=1E-8), a plain cut-off or switch function for LJ interactions (neighborlist updated on every time step for test purposes), and double precision. At least there hasn't been such problems with these parameters (excluding pure LJ cut-off) earlier with other systems. New features in this system for me are positions restraints which are used for some atoms (160 of 46080 atoms) to maintain "original crystal shape" and option pbc=full due to the infinite chains. Could it be that position restraints or full periodic boundary conditions are responsible for the energy drift or should I just still try to equilibriate system more in NVT ensemble? I guess that this could be the problem, because there seems to be also some huge problems depending on number of processors used for the simulation. Simulation with 2 processors progresses normally although energy drift is observed, but with 4 processors simulation terminates pretty soon and huge momentary increases in energy in intervals of 0.05ps can be observed earlier. Thanks for any help, Janne _______________________________________________ gmx-users mailing list gmx-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
