> > On 4/3/17 2:33 PM, Dayhoff, Guy wrote: >> >>>> Hi, >>>> >>>> I?m receiving a couple (~15) EM did not converge warnings as well as a >>>> few (~3) 1,4 interaction >>>> warnings during my run. It looks like it starts down the path to blowing >>>> up but recovers. Is this ?recovery? >>>> system dependent? Should I take these messages (even without the >>>> subsequent crash) to indicate an >>>> underlying issue with my system/topology or equilibration? I?m not >>>> ignoring or circumventing any warning >>>> during pdb2gmx, or any other commands. >>>> >>>> For more context: I?m running the Drude-2013 forcefield, with a dt of .5fs >>>> emtol of 1.0 and niter of 150 >>>> using the V-rescale thermostat and Berendsen pressure coupling while my >>>> systems cell shape relaxes >>>> as a continuation from position restrained NVT then NPT ensembles. The >>>> starting structures were minimized >>>> in vacuum, then solvated and minimized once again prior to the posres >>>> equilibration. >>>> >>> >>> Such a short dt and strict niter should not be necessary in practice. The >>> failure of SCF to converge/LINCS warnings is what we typically refer to as >>> polarization catastrophe, so your system is on the brink of instability. >>> This >>> is one of the inherent problems of SCF in polarizable systems; it often >>> fails to >>> converge and leaves the system potentially unstable. The reflective >>> hardwall is >>> much more reliable (and faster). If the instability is happening in your >>> equilibration, that may be OK but it is something you should try to >>> troubleshoot >>> to make sure there's nothing else going wrong. >>> >>> -Justin >>> >>> -- >>> >> >> Got it. I have been spending some time investigating the issue i?m having and >> after reading shellfc.cpp I was pretty confident the issue was with SCF not >> converging, >> and so my niter and dt were an attempt at looking into that. >> >> The workflow i?ve been trying to use is? >> EM -> Solvate -> EM -> posres NVT V-rescale -> posres berendsen NPT >> isotropic 1bar w/ V-rescale tcoupl -> >> berendsen NPT semi-isotropic various pressures w/ V-rescale tcoupl >> >> then once my cell shape has reached an equilibrium I finally switch to NH >> thermostat and PR barostat for >> the production run. >> >> If I switch to employing the hardwall (and the lagrangian dynamics for >> drudes) then I understand it is not >> compatible yet with NPT ensembles. So, if I change my work flow as follows >> would it be appropriate still? >> >> EM->Solvate->EM->posre NPT isotropic 1 bar w/ V-rescale tcoupl->NPT >> semi-isotropic varying pressures >> w V-rescale tcoupl until cell shape is equilibrated using PR barostat, then >> switch to NVT without pcoupl >> to use the hardwall during my production run? >> >> For some reason, i?ve got this idea that I need to be tcoupling and >> pcoupling during my production runs >> so i?ve been apprehensive to do this. >> > > If you want an NPT ensemble during dynamics you're going to have to use NAMD, > CHARMM, or OpenMM. I haven't coded the barostat yet (fixing the DD bugs has > been more important). You can equilibrate with SCF under NPT and get a > suitable > density, then switch to NVT, but your use of semi-isotropic coupling suggests > a > membrane system? In that case, I would not use NVT during production as you > will be simulating a constant area, which may not be appropriate. >
I’ve parameterized beta-cellulose and then an additional modified form of beta-cellulose for the FF and i’m looking at the packing behavior of a bundle of strands under the different pressures in water. Everything seems to be proper apart from encountering the polarization catastrophe randomly, often times I can restart a downed run and it will move beyond the previous crash point, but this is tedious and even when I wrote a script to do it for me I found that eventually there was a point of no return, even if I used the prev_cpt. I was able to run a single 20mer strand for 2ns without a crash, but my actual system has many strands in it. Does scalability come into play here, my system is near 60k atoms? I know these features are not supported officially yet, are there any suggestions pertaining to a possible source of error to check that I wouldn’t have come across in the documentation or other forums? I’ve been wrestling with getting the production runs going for a few weeks, perhaps its time to just move to another simulation suite as you mentioned which has full implementation of the drude oscillators. - Guy -- 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.
