On 25.04.2014 00:07, Ricardo O. S. Soares wrote:
I ran an NVT equilibration of a 24mi CG Martini atoms and detected the formation of vacuum spots on the solvent.
CG Martini has many sphere types, did you solvate your system with 24x10^6 MARTINI-W segments? MARTINI-W is is strongly association LJ-fluid. In large, inhomogeneous systems (non-optimal box solvation) it is expected to generate huge forces if either too-close or not close enough packed.
However, the log file shows a very large negative pressure (about -4e+28) all the time, since the beginning. Despite the negative pressure, when I turn pressure coupling ON, the very first step causes the box to expand (!) too much and then the simulation crashes.
there you are ...
Things I tried, and failed: changed the tau_p to several values (1 to 500); changed the compressibility; changed the ref_p from 1 to values closer to the starting pressure; changed time-step from 0.02 up to 0.0005. Additional info: used the insane.py script to solvate the box with polarizable water; there's a large (frozen) bilayer at the center of the box, It, however is smaller than the box sides, to it doesn't interact with itself via PBC. I'm sure I could provide more info, so please ask me for the specifics and I'll reply.
How large is the box, is it cubic? How many Lipids in the bilayer? What do you expect from the frozen bilayer if you pressure-couple your box dimensions? Be warned that the MARTINI-Lipids constitute bilayers which are very "floppy" and spontaneously fold into spheres (vesicles) if the aggregate has more than around 600 Molecules. BTW.: what hardware are you on if you expect to equilibrate a system of that size (if the 2.4x10^6 figure is correct?) Regards M. Disclaimer: I did simulate similar MARTINI systems of 1/10th the size of yours -- 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.
