[gmx-users] LINCS warning: "Relative constraint deviation after LINCS"
David van der Spoel
spoel at xray.bmc.uu.se
Wed Nov 12 09:11:01 CET 2003
On Wed, 2003-11-12 at 00:09, Martina Bertsch, PhD wrote:
> Hi, David.
>
> I have made the changes you suggested (see below for the modified
> *pr.mdp). By the way,
>
> to make a group of POPC+Protein for center-of-mass motion removal, I added a line:
>
> comm_grps = protein+popc sol
>
> Is this all I have to do, or do I need to define the group protein+popc somewhere else?
>
No you will have to use make_ndx to create a combined group.
> The mdrun stops at step 0. A LINCS warning appears about a relative
> constraint deviation after LINCS:
> max 227.983810 (between atoms 3223 and 3224) rms 4.787549.
> Atoms 3223 and 3224 belong to a POPC tail.
> Then it lists a bunch of bonds that rotated more than 30 degrees (all in
> POPCs).
>
This is weird, there is probably still something wrong with your
starting structure. Check in the input structure the distance between
these atoms. Judging from the numbers you gave below it starts out all
right, so it's most like large forces due to close contacts that cause
problems.
> Does this mean that I have go back to the CG-EM step and use the double
> precision libs?
> Do I need to manually remove additional lipid molecules from the hole?
> Or, do I rerun Tieleman-Smith's mdrun for a shorter time (currently
> using hfm=25 and timestep 2 fs for 10 ps) or perhaps increase both hfm
> and time?
It maybe necessary to edit your topology manually. If you are brave you
could consider using soft-core potential to equilibrate a bit before.
Creating a big hole is also undesirable as it will take a long time to
fill the holes.
>
> The GPCR_popc_pr.log file reads:
>
> ...
> Initializing LINear Constraint Solver
> number of constraints is 8698
> average number of constraints coupled to one constraint is 2.5
>
> Rel. Constraint Deviation: Max between atoms RMS
> Before LINCS 1.225229 3223 3224 0.021533
> After LINCS 0.094904 3397 3398 0.002627
>
>
> Step -2, time -0.002 (ps) LINCS WARNING
> relative constraint deviation after LINCS:
> max 0.094904 (between atoms 3397 and 3398) rms 0.002627
> bonds that rotated more than 30 degrees:
> atom 1 atom 2 angle previous, current, constraint length
> 3222 3223 36.2 0.1447 0.1612 0.1530
> 3224 3225 40.6 0.1458 0.1626 0.1530
> Going to use C-settle (2460 waters)
> wo = 0.888096, wh =0.0559521, wohh = 18.0154, rc = 0.081665, ra = 0.00645837
> rb = 0.051255, rc2 = 0.16333, rone = 1, dHH = 0.16333, dOH = 0.1
>
> Constraining the coordinates at t0-dt (step -1)
> Rel. Constraint Deviation: Max between atoms RMS
> Before LINCS 0.095785 3223 3224 0.006243
> After LINCS 0.858278 3397 3398 0.016634
>
>
> Step -1, time -0.001 (ps) LINCS WARNING
> relative constraint deviation after LINCS:
> max 0.858278 (between atoms 3397 and 3398) rms 0.016634
> bonds that rotated more than 30 degrees:
> atom 1 atom 2 angle previous, current, constraint length
> 3395 3398 76.2 0.1341 0.0446 0.1470
> 3398 3399 78.8 0.1341 0.0492 0.1470
> Constraint error in algorithm Lincs at step -1
> Started mdrun on node 0 Tue Nov 11 16:39:45 2003
>
> Initial temperature: 1041.92 K
> Grid: 20 x 20 x 20 cells
> calc_bor: cg0=0, cg1=8311, ncg=8311
> CG0[0]=0, CG1[0]=8311
> CG0[1]=0, CG1[1]=0
> calc_bor: cg0=0, cg1=8311, ncg=8311
> CG0[0]=0, CG1[0]=8311
> CG0[1]=0, CG1[1]=0
>
> Testing x86 processor CPUID...
>
> Testing x86 SSE capabilities...
> CPU and OS support SSE.
> Using Gromacs SSE single precision assembly innerloops.
>
> Step Time Lambda Annealing
> 0 0.00000 0.00000 1.00000
>
> There are 16130 atoms in your xtc output selection
> Rel. Constraint Deviation: Max between atoms RMS
> Before LINCS 300.089874 1455 1456 6.559021
> After LINCS 227.983810 3223 3224 4.787549
>
>
> Step 0, time 0 (ps) LINCS WARNING
> relative constraint deviation after LINCS:
> max 227.983810 (between atoms 3223 and 3224) rms 4.787549
>
> Atoms 3223 and 3224 belong to a POPC tail.
>
> Then it lists a bunch of bonds that rotated more than 30 degrees (all in
> POPCs).
>
> Constraint error in algorithm Lincs at step 0
> Large VCM(group POPC): 0.00001, 0.00001, -0.00001,
> ekin-cm: 0.00001
> Large VCM(group SOL): 0.00117, -0.00468, 0.00983,
> ekin-cm: 2.65573
> Large VCM(group rest): -4.17806, -4.86114, 4.32485,
> ekin-cm: 924022.43750
> Energies (kJ/mol)
> Angle Proper Dih. Ryckaert-Bell. Improper Dih. LJ-14
> 3.09203e+04 6.34127e+03 4.56703e+03 5.86512e+03 9.30483e+03
> Coulomb-14 LJ (SR) LJ (LR) Coulomb (SR) Coulomb (LR)
> 3.79305e+04 7.64607e+06 -1.32418e+03 -1.44977e+05 -1.49079e+05
> Position Rest. Potential Kinetic En. Total Energy Temperature
> 1.78889e+01 7.44563e+06 2.68355e+09 2.69099e+09 1.99829e+07
> Pressure (bar)
> 1.66548e+07
>
> Thank you very much.
>
> Kind regards,
>
> Martina Bertsch, Ph.D.
> Northwestern University
> Feinberg School of Medicine
> Molecular Pharmacology and Biological Chemistry
> 303 East Chicago Avenue
> Chicago, IL 60611
>
>
> David wrote:
>
> >
> >Hm, no obvious mistakes, you might want to remove the -DFLEX_SPC, and to
> >make a group of POPC+Protein for center-of-mass motion removal.
> >
> >In which molecule do you get the lincs error? (print the rest of the
> >message, if it doesn't show try mdrun -v or even mdrun -v -debug).
> >
> >>>>
> >>>>
> >>>>
> >>>>______________________________________________________________________
> >>>>
> >>>>title = GPCR in POPC PR-MD
> >>>>cpp = /lib/cpp
> >>>>define = -DPOSRES
> >>>>constraints = all-bonds
> >>>>constraint_algorithm = lincs
> >>>>integrator = md
> >>>>dt = 0.001 ; ps !
> >>>>ns
> >>>>teps = 5000000 ; total 5 ns
> >>>>;nstcomm = 1
> >>>>nstxout = 5000
> >>>>nstvout = 5000
> >>>>nstfout = 5000
> >>>>nstlog = 5000
> >>>>nstenergy = 5000
> >>>>nstxtcout = 5000
> >>>>nstlist = 10
> >>>>ns_type = grid
> >>>>rlist = 1.0
> >>>>coulombtype = PME
> >>>>rcoulomb = 1.0
> >>>>rvdw = 1.2
> >>>>pbc = xyz
> >>>>comm_mode = linear
> >>>>nstcomm = 1
> >>>>fourierspacing = 0.15
> >>>>pme_order = 4
> >>>>optimize_fft = yes
> >>>>comm_grps = protein+popc sol
> >>>>; Berendsen temperature coupling is on in two groups
> >>>>Tcoupl = berendsen
> >>>>tau_t = 0.1 0.1 0.1
> >>>>tc-grps = protein popc sol
> >>>>ref_t = 300 300 300
> >>>>; Energy monitoring
> >>>>energygrps = protein popc sol
> >>>>; Pressure coupling is on
> >>>>Pcoupl = berendsen
> >>>>pcoupltype = anisotropic
> >>>>tau_p = 5 5 5 0 0 0
> >>>>compressibility = 4.5e-5 4.5e-5 4.5e-5 0 0 0
> >>>>ref_p = 1.0 1.0 1.0 0 0 0
> >>>>; Generate velocites is on at 300 K.
> >>>>gen_vel = yes
> >>>>gen_temp = 300.0
> >>>>gen_seed = 280572
> >>>>
>
>
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--
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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