[gmx-users] AlF4 - producing LINCS errors
Mark Abraham
mark.abraham at anu.edu.au
Mon Feb 28 12:24:14 CET 2011
On 02/28/11, Matthew Cliff <m.j.cliff at sheffield.ac.uk> wrote:
> Hi,
>
> I'm very new to MD and I am trying to run MD simulations of proteins binding AlF4-. I am running GROMACS 4.5.3
> and using OPLSAA forcefield, Tip4p water.
> I have created a topology file for AlF4 (see below), and added atom types to the forcefield files atomtypes and ffnonbonded (see bottom of topology file). The force constants are pretty much fictitious, but I think reasonable.
>
> If I run the AlF4- in a box of water with a counterion (Na+) with timestep 1fs and constraints=none then nothing untoward happens. However, if I run with 2 fs time step and constraints=all-bonds, then it goes horribly wrong after 69 steps and says:
> "Step 69, time 0.138 (ps) LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.211433, max 0.232176 (between atoms 2 and 5)
> bonds that rotated more than 30 degrees:
> atom 1 atom 2 angle previous, current, constraint length
>
> Step 70, time 0.14 (ps) LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.558220, max 0.947733 (between atoms 2 and 4)
> bonds that rotated more than 30 degrees:
> atom 1 atom 2 angle previous, current, constraint length
> 2 1 142.7 0.1413 0.1214 0.1790
> 2 5 166.0 0.1374 0.1126 0.1790
> 2 3 142.6 0.1416 0.1203 0.1790
> Wrote pdb files with previous and current coordinates"
>
> If I increase the bond strength this takes longer, but still happens. Energy minimisation works fine (of course?).
>
> Obviously I would like to do half the calculations. (md.mdp is also at the bottom of this e-mail)
>
> Cheers,
>
> Matt Cliff
>
>
>
> [ moleculetype ]
> ; Name nrexcl
> ALF 3
>
> [ atoms ]
> ; charges need to be checked
> ; nr type resnr resid atom cgnr charge mass
> 1 opls_998 1 ALF F1 1 -0.8 18.99840 ;Al etc
> 2 opls_997 1 ALF AL 1 2.2 26.98153 ;Al etc
> 3 opls_998 1 ALF F2 1 -0.8 18.99840 ;Al etc
> 4 opls_998 1 ALF F3 1 -0.8 18.99840 ;Al etc
> 5 opls_998 1 ALF F4 1 -0.8 18.99840 ;Al etc
>
> [ bonds ]
> ; ai aj fu b0, kb, ...
> 2 1 1 0.179 87864.0 0.179 87864.0 ; Al-F
> 2 3 1 0.179 87864.0 0.179 87864.0 ; Al-F
> 2 4 1 0.179 87864.0 0.179 87864.0 ; Al-F
> 2 5 1 0.179 87864.0 0.179 87864.0 ; Al-F
>
> [ angles ]
> ; ai aj ak fu c0, c1, ...
> 1 2 4 1 90 397.5 90.0 397.5
> 1 2 3 1 180 397.5 180.0 397.5
> 1 2 5 1 90 397.5 90.0 397.5
> 3 2 4 1 90 397.5 90.0 397.5
> 3 2 5 1 90 397.5 90.0 397.5
> 4 2 5 1 180 397.5 180.0 397.5
>
I'd be suspicious of those 180-degree angles. They are trouble for linear species like nitriles. Depending how the angles are computed and used, enforcing a bond constraint could be flipping one from -180 to +180. I think you need only use 4 90-degree angles and 2 planarity-enforcing dihedrals. In extremis, maybe define the Al as a COM virtual site. (See manual).
Mark
> [ dihedrals ]
> ; ai aj ak al fu c0, c1, m, ...
> 2 3 1 4 2 0.0 1673.6 0.0 1673.6 ; imp making it flat
> 2 1 4 5 2 0.0 1673.6 0.0 1673.6 ; imp making it flat
>
> #ifdef POSRES
> [ position_restraints ]
> 1 1 1000 1000 1000
> 2 1 1000 1000 1000
> 3 1 1000 1000 1000
> 4 1 1000 1000 1000
> 5 1 1000 1000 1000
> #endif
>
>
> In atomtypes.atp:
> opls_997 26.98153 ; Al
> opls_998 18.99840 ; F
>
> In ffnonbonded.itp:
> opls_998 F 9 18.9984 -1.00 A 2.9500e-01 2.22e-01
> opls_997 AL 13 26.98153 3.00 A 1.0e-01 3.66e+00 ;
>
> ; Input file
> ;
> title = General
> cpp = /usr/bin/cpp -traditional
> constraints = all-bonds
> integrator = md
> dt = 0.002 ; ps !
> nsteps = 10000 ; total 2 ns
> nstcomm = 1
> nstcalcenergy = 1
> nstxout = 500
> nstvout = 500
> nstfout = 0
> nstxtcout = 5000
> nstlog = 1000
> nstenergy = 1000
> nstlist = 5
> ns_type = grid
> rlist = 1.2
> rcoulomb = 1.2
> coulombtype = pme
> vdwtype = cut-off
> rvdw = 1.2
> optimize_fft = yes
> DispCorr = EnerPres
> ; V-rescale temperature coupling is on in two groups
> Tcoupl = v-rescale
> tc-grps = Other Water_and_ions
> tau_t = 0.1 0.1
> ref_t = 300 300
> ; Energy monitoring
> energygrps = Other Water_and_ions
> ; Isotropic pressure coupling is now on
> Pcoupl = berendsen
> Pcoupltype = isotropic
> tau_p = 1.0
> compressibility = 4.5e-5
> ref_p = 1.0
> ; Generate velocites is off (from traj)
> gen_vel = no
> gen_temp = 300.0
> gen_seed = 173529
>
> --
> Dr. Matthew J Cliff
> Tel: (0114) 2222708
> e-mail: m.j.cliff at sheffield.ac.uk
> Molecular Biology and Biotechnology
> University of Sheffield
> Firth Court
> Western Bank
> Sheffield
> S10 2TN
> UK
>
> --
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