Hi, I am simulating DNA (infinite) protein Martini system with electric field. I have 2 systems, for 1 complete DNA is frozen and for the 2nd one, only 4 atoms of the DNA is frozen. When I perform NPT equilibration for the complete DNA frozen system, it shows me this error :
Fatal error: 4442 particles communicated to PME rank 24 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension y. This usually means that your system is not well equilibrated. But it runs fine for the other system with 4 DNA atoms frozen. For the completely frozen DNA, if I freeze only 2 dimensions, letting 1 dimension free it runs without complaining. I do not understand why it shows problem for the completely frozen DNA with 3 dimensions frozen? Since the DNA is infinite I use semi-isotropic pressure coupling keeping the compressibility along Z 0. So the pressure coupling options in my .mdp file looks like this : freezegrps = DNA freezedim = Y N Y ; Pressure coupling is off ;pcoupl = no ; no pressure coupling in NVT Pcoupl = parrinello-rahman Pcoupltype = semiisotropic tau_p = 5.0 compressibility = 3e-4 0 ref_p = 1.0 1.0 refcoord_scaling = all I tried it for finite DNA too and it shows same problem for completely frozen DNA. I ran the completely Frozen DNA system keeping 1 dimension free, and freezing the other 2 dimensions. I ran the equilibration run for 500 ps. I plotted the pressure and the average pressure is 9.15 bar, while the target pressure that I had put in the .mdp file is 1 bar. So there is a large difference. I was searching regarding this problem, and I found that I need to use "energygrp-excl" for frozen groups. So I ran the completely frozen DNA system with energygrp-excl = DNA, using cutoff-scheme = group (since energygrp-excl is not supported in Verlet in my gromacs version 5.0.6), and the average pressure I get is again 9.28 bar. For the system with 4 DNA atoms frozen, the average pressure shows 5.17 bar, which is still different from the target pressure. I am now running these equilibration runs for longer (4 ns), to see if that helps to get the average pressure closer to 1 bar. Normally when all atoms are free what I found was 0.5 ns was enough to get average pressure 1 bar, and equilibrate the system. But I don't understand what is the problem I am facing here with frozen atoms? I turn off the electric field during the equilibration runs. I would highly appreciate any help! Thank you very much, Regards, Arnab -- 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.