[gmx-users] Lincs all-bonds causing instability in otherwise stable system
Mark Abraham
mark.j.abraham at gmail.com
Wed May 20 13:47:48 CEST 2015
Hi,
Sorry that was so painful for you. The LINCS documentation in the manual
suggests that that combination of bonds becoming constraints won't work
well. Perhaps we should add a 3-edge cycle detector to grompp?
If you actually want a rigid planar DMSO, then three real atoms and a
virtual site would be the best implementation.
Mark
On Wed, May 20, 2015 at 6:41 AM Cara Kreck <cara.kreck at student.curtin.edu.au>
wrote:
> Hi everyone,
>
> I never got a reply to my message but I figured out the problem by myself.
> Just in case anyone else runs into a similar problem I thought I should
> explain what was wrong and share the solution.
>
> I was using a DMSO topology from the ATB that uses extra bonds to fix the
> geometry instead of angle or dihedral terms:
>
> [ moleculetype ]
> ; Name nrexcl
> DMSO 3
> [ atoms ]
> ; nr type resnr resid atom cgnr charge mass total_charge
> 1 SDmso 1 DMSO S 1 0.128 32.0600
> 2 ODmso 1 DMSO O 1 -0.448 15.9994
> 3 CDmso 1 DMSO C 1 0.160 15.0350
> 4 CDmso 1 DMSO C 1 0.160 15.0350 ; 0.000
> ; total charge of the molecule: 0.000
> [ bonds ]
> ; ai aj funct c0 c1
> 1 2 2 0.1530 8.0400e+06
> 1 3 2 0.1938 4.9500e+06
> 1 4 2 0.1938 4.9500e+06
> 2 3 2 0.2794 2.3900e+06
> 2 4 2 0.2794 2.3900e+06
> 3 4 2 0.2912 2.1900e+06
>
> This topology is fine to use with SHAKE but LINCS doesn't seem to be able
> to handle it. When I removed the extra bonds my simulations were able to
> run with all bonds constrained by LINCS. Then I found appropriate angle and
> dihedral parameters in the GROMOS ffbonded.itp file to control the geometry
> again. My topology file now looks like this:
>
> [ moleculetype ]
> ; Name nrexcl
> DMSO 3
> [ atoms ]
> ; nr type resnr resid atom cgnr charge mass total_charge
> 1 SDmso 1 DMSO S 1 0.128 32.0600
> 2 ODmso 1 DMSO O 1 -0.448 15.9994
> 3 CDmso 1 DMSO C 1 0.160 15.0350
> 4 CDmso 1 DMSO C 1 0.160 15.0350 ; 0.000
> ; total charge of the molecule: 0.000
> [ bonds ]
> ; ai aj funct c0 c1
> 1 2 2 0.1530 8.0400e+06
> 1 3 2 0.1938 4.9500e+06
> 1 4 2 0.1938 4.9500e+06
> [ angles ]
> ; ai aj ak funct angle fc
> 3 1 4 2 97.40 469.00
> 3 1 2 2 106.75 503.00
> 4 1 2 2 106.75 503.00
> [ dihedrals ]
> ; GROMOS improper dihedrals
> ; ai aj ak al funct angle fc
> 1 3 4 2 2 35.26439 334.84617 ; tetrahedral centre
>
> I ran an energy minimisation of a single molecule with the new topology
> and its geometry overlapped the old one perfectly. So the problem was
> difficult to diagnose but easy to fix. Especially since I was able to
> energy minimise the individual molecules with all bonds constrained but the
> constraints went haywire when everything was combined in the full system.
> Hopefully I can at least save someone else from wasting 3 weeks trying to
> get a similar topology to work with LINCS.
>
> Cara
>
>
> > From: cara.kreck at student.curtin.edu.au
> > To: gromacs.org_gmx-users at maillist.sys.kth.se
> > Date: Fri, 15 May 2015 14:31:16 +0800
> > Subject: [gmx-users] Lincs all-bonds causing instability in otherwise
> stable system
> >
> > I forgot to include an example of my mdp files. I've tried varying the
> timestep, running with and without pressure coupling, and obviously
> changing the constraints as outlined in the previous message:
> >
> > integrator = md
> > dt = 0.001 ; 1fs
> > nsteps = 100000 ; 100ps
> > 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
> > constraints = all-bonds
> > constraint_algorithm = shake
> > continuation = yes
> >
> >
> > > From: cara.kreck at student.curtin.edu.au
> > > To: gromacs.org_gmx-users at maillist.sys.kth.se
> > > Date: Fri, 15 May 2015 14:17:28 +0800
> > > Subject: [gmx-users] FW: Lincs all-bonds causing instability in
> otherwise stable system
> > >
> > > Hi,
> > >
> > > I am having trouble constraining all-bonds with lincs in a system that
> is stable using shake all-bonds or lincs h-bonds in gromacs 4.6.7. The
> previous step using lincs h-bonds gave these energies:
> > >
> > > Step Time Lambda
> > > 200000 200.00000 0.00000
> > >
> > > Energies (kJ/mol)
> > > G96Bond G96Angle Proper Dih. Improper Dih.
> LJ-14
> > > 1.76317e+04 2.43132e+04 1.39308e+04 1.55159e+03
> -2.91002e+03
> > > Coulomb-14 LJ (SR) LJ (LR) Coulomb (SR) Coulomb
> (LR)
> > > 4.07560e+05 -4.09017e+03 -1.26700e+04 -5.62217e+05
> -3.06259e+03
> > > RF excl. Potential Kinetic En. Total Energy
> Temperature
> > > -1.24406e+05 -2.44368e+05 9.29185e+04 -1.51450e+05
> 3.02522e+02
> > > Pressure (bar) Constr. rmsd
> > > -1.98735e+02 1.95240e-06
> > >
> > > However, when I switch to lincs all-bonds the 0 step kinetic energy,
> temperature, and pressure are dramatically increased, even though
> continuation=yes and gen_vel=no. The system then quickly crashes. I tried
> using GMX_MAXCONSTRWARN=-1 and particle decomposition to get past the
> errors but then it simply stalls without crashing or outputting anything.
> > >
> > > Step Time Lambda
> > > 0 0.00000 0.00000
> > >
> > > Grid: 8 x 8 x 14 cells
> > > Energies (kJ/mol)
> > > G96Angle Proper Dih. Improper Dih. LJ-14
> Coulomb-14
> > > 2.43132e+04 1.39308e+04 1.55159e+03 -2.91002e+03
> 4.07560e+05
> > > LJ (SR) LJ (LR) Coulomb (SR) Coulomb (LR) RF
> excl.
> > > -4.09017e+03 -1.26700e+04 -5.62217e+05 -3.06259e+03
> -1.24406e+05
> > > Potential Kinetic En. Total Energy Temperature Pressure
> (bar)
> > > -2.62000e+05 4.92862e+05 2.30862e+05 1.93783e+03
> 1.04858e+04
> > > Constr. rmsd
> > > 1.44601e-02
> > >
> > > When I instead switch to shake all-bonds (with particle decomposition)
> I get a similar spike in the kinetic energy etc. but the system is able to
> recover without crashing. Unfortunately gromacs won't let me use pressure
> coupling with shake due to my twin-range cut-offs though, so I need to find
> a way to get lincs to work. I tried switching to lincs all-bonds after
> 100ps with shake all-bonds, and there was no longer the spike in energies
> except for the pressure:
> > >
> > > Step Time Lambda
> > > 100000 100.00000 0.00000
> > >
> > > Energies (kJ/mol)
> > > G96Angle Proper Dih. Improper Dih. LJ-14
> Coulomb-14
> > > 2.46619e+04 1.38286e+04 1.50388e+03 -2.92380e+03
> 4.11368e+05
> > > LJ (SR) LJ (LR) Coulomb (SR) Coulomb (LR) RF
> excl.
> > > -3.50689e+03 -1.26695e+04 -5.64100e+05 -2.81505e+03
> -1.24427e+05
> > > Potential Kinetic En. Total Energy Temperature Pressure
> (bar)
> > > -2.59079e+05 7.73473e+04 -1.81732e+05 3.04114e+02
> -4.16208e+02
> > >
> > > Step Time Lambda
> > > 0 0.00000 0.00000
> > >
> > > Energies (kJ/mol)
> > > G96Angle Proper Dih. Improper Dih. LJ-14
> Coulomb-14
> > > 2.46619e+04 1.38286e+04 1.50388e+03 -2.92380e+03
> 4.11368e+05
> > > LJ (SR) LJ (LR) Coulomb (SR) Coulomb (LR) RF
> excl.
> > > -3.50690e+03 -1.26695e+04 -5.64100e+05 -2.81533e+03
> -1.24427e+05
> > > Potential Kinetic En. Total Energy Temperature Pressure
> (bar)
> > > -2.59079e+05 7.73979e+04 -1.81681e+05 3.04313e+02
> 5.61153e+02
> > > Constr. rmsd
> > > 2.45638e-04
> > >
> > > However, it still crashes with a domain decomposition error. When I
> switch back to particle decomposition it stalls again. I then tried
> decreasing the time-step to 0.1fs and I got lots of these errors before
> stalling:
> > >
> > > WARNING: Listed nonbonded interaction between particles 2485 and 2490
> > > at distance 3f which is larger than the table limit 3f nm.
> > >
> > > This is likely either a 1,4 interaction, or a listed interaction inside
> > > a smaller molecule you are decoupling during a free energy calculation.
> > > Since interactions at distances beyond the table cannot be computed,
> > > they are skipped until they are inside the table limit again. You will
> > > only see this message once, even if it occurs for several interactions.
> > >
> > > IMPORTANT: This should not happen in a stable simulation, so there is
> > > probably something wrong with your system. Only change the
> table-extension
> > > distance in the mdp file if you are really sure that is the reason.
> > >
> > > There were 156 inconsistent shifts. Check your topology
> > > There were 190 inconsistent shifts. Check your topology
> > >
> > >
> > > Whereas with domain decomposition and a 0.1 fs time-step it still
> crashes with a domain decomposition error. I don't understand why a system
> that is perfectly fine with lincs h-bonds and shake all-bonds can be so
> problematic with lincs all-bonds. Any suggestions?
> > >
> > > Thanks,
> > >
> > > Cara
> >
> >
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