[gmx-users] LINCS warnings for a single molecule in otherwise stable system

Thu Jul 2 12:58:30 CEST 2015

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.abraham at gmail.com
> Date: Thu, 2 Jul 2015 10:42:23 +0000
> To: gmx-users at 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.kreck at 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
> >
> >
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