On 02/28/11, Matthew Cliff <m.j.cl...@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.cl...@sheffield.ac.uk > Molecular Biology and Biotechnology > University of Sheffield > Firth Court > Western Bank > Sheffield > S10 2TN > UK > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >
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