[gmx-users] LINCS warning: "Relative constraint deviation after LINCS"
Martina Bertsch, PhD
mbe404 at lulu.it.northwestern.edu
Wed Nov 12 00:06:01 CET 2003
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?
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).
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?
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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