Hi Peter, Thank you very much for your suggestion. I will try using atom restraints and check if the pressure coupling works properly.
Thanks and regards, Arnab. On Sep 11, 2018 10:33 AM, "Peter Kroon" <p.c.kr...@rug.nl> wrote: > Hey Arnab, > > > Why do you freeze atoms instead of putting position restraints? Why not > let the loose entirely? Freezing creates large artefacts. > > Second, 4 ns equilibration is *way* too short. > > Lastly, see http://www.gromacs.org/Documentation/Terminology/Pressure > > > Peter > > > On 10-09-18 19:01, ARNAB MUKHERJEE wrote: > > 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. > -- 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.