Hi, While we can't exclude the possibility of a code bug, your analysis and results suggest the problem lies elsewhere. Is the EG model stable if you e.g. put one in a box of decane? It's a stab in the dark, but if EG was parameterized only for aqueous-phase properties, then all bets are off once it gets into the membrane...
Mark On Thu, Jul 2, 2015 at 12:35 PM Cara Kreck <cara.kr...@student.curtin.edu.au> wrote: > Hi everyone, > > I am trying to run a simulation of a lipid bilayer with a multi-component > solution. One of the components is ethylene glycol. Some of the components > have a tendency to wriggle their way into the lipids. When an EG molecule > does this, it tends to get uncomfortable and trigger some LINCS warnings. > It only happens with a single EG molecule at a time. It never happens with > any of the other components or the EG molecules in the solution. It never > leads to anything else becoming unstable or the system blowing up, it just > causes a crash when the warning limit is reached. The strangest thing is > when the simulation is continued from the checkpoint, the problem goes away > for a while but eventually reoccurs within a few hours with a completely > different EG molecule wedged in the membrane. > > I have tried increasing both lincs-order and lincs-iter, but it still > happens. I have tried increasing lincs-warnangle, but that just lets the > angle fluctuations get bigger before the job is killed. I tried using a > slightly different topology for EG and I thought that had helped for a > while. The first time the angle fluctuations started, they stayed around > the 30 degrees mark and went away by themselves after around 600 warnings, > so the job was then able to run for the full 24 hours allowed. The last 2 > jobs I have submitted have been killed prematurely by LINCS warnings that > didn't go away by themselves though. This is very frustrating as I am > running on a very busy cluster and it can take 24-48 hours for a job to > progress through the queue, only to then be killed within a couple of hours > of running. The only thing I can think of now is to increase > lincs-warnangle by a small amount so that the smaller fluctuations are > given a chance to sort themselves out before being killed. > > If anyone else could give me any suggestions, I would really appreciate > it. I am using GROMACS 4.6.7 and the GROMOS53A6 FF. Here is a copy of my > mdp file: > > integrator = md > dt = 0.002 ; 2fs > nsteps = 500000000 ; 1000 ns > comm_grps = DOPC !DOPC > nstxout = 1000 > nstvout = 0 > nstlog = 1000 > nstenergy = 1000 > energygrps = DOPC !DOPC > nstcalcenergy = 5 > nstlist = 5 > ns_type = grid > pbc = xyz > rlist = 0.8 > coulombtype = Reaction-Field > rcoulomb = 1.4 > epsilon_rf = 62 > vdwtype = Cut-off > rvdw = 1.4 > tcoupl = berendsen > tc-grps = DOPC !DOPC > tau_t = 0.1 0.1 > ref_t = 303 303 > Pcoupl = berendsen > pcoupltype = semiisotropic > tau_p = 1.0 1.0 > compressibility = 4.6e-5 4.6e-5 > ref_p = 1.0 1.0 > gen_vel = no > gen_temp = 150 > gen_seed = 173529 > constraints = all-bonds > constraint_algorithm = lincs > lincs-order = 6 > lincs-iter = 2 > continuation = yes > > Thanks, > > Cara > > > -- > 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.