Hi Mark, I'll give it a shot and see. One other thing I forgot to mention is that the first EG topology has been successfully used for membrane simulations in GROMACS 3.3.3 using SHAKE. I am continuing this work but wanted to use GROMACS 4.6.7 to speed things up. Unfortunately GROMACS 4.6.7 won't let me use SHAKE with reaction field and pressure coupling, which is why I am now using LINCS.
Thanks, Cara > From: mark.j.abra...@gmail.com > Date: Thu, 2 Jul 2015 10:42:23 +0000 > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] LINCS warnings for a single molecule in otherwise > stable system > > 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. -- 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.