[gmx-users] AlF4 - producing LINCS errors
Matthew Cliff
m.j.cliff at sheffield.ac.uk
Mon Feb 28 18:18:10 CET 2011
Thanks, that solved it!
On 28/02/11 11:24, Mark Abraham wrote:
>
>
> 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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--
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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