[gmx-users] LINCS WARNING relative constraint deviation
Justin Lemkul
jalemkul at vt.edu
Mon Oct 1 14:52:41 CEST 2012
On 10/1/12 7:10 AM, Ali Alizadeh wrote:
> Dear all users
>
> 1- I am trying to simulate a system that contains 1182 methane
> molecules(5910 atoms) and 1830 water molecules(5490), I
> keep getting these errors.
Something is wrong with the starting configuration, topology, or .mdp settings
(see below for comments) such that energy minimization fails almost instantly.
http://www.gromacs.org/Documentation/Terminology/Blowing_Up
> 2- Gromacs does not give me a .xtc file, Why?
Perhaps there's some quirk of the code that won't produce an .xtc file with an
EM algorithm. EM is normally quick and takes up little disk space, so the
benefit to having a compressed trajectory is minimal in most cases.
> My command lines for grompp and mdrun in terminal window:
>
> grompp -f npt.mdp -c wwfull.top.gro -p topol.top -o topol.tpr -n ww.ndx
> mdrun -s topol.tpr -o wwfull.trr -x wwfull.xtc
>
> These are errors and my .mdp file:
>
> ...........................................
> Steepest Descents:
> Tolerance (Fmax) = 1.00000e-04
> Number of steps = 1000
>
> Step 50, time 0.01 (ps) LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.000589, max 0.014000 (between atoms 2636 and 2638)
> bonds that rotated more than 30 degrees:
> atom 1 atom 2 angle previous, current, constraint length
> 2636 2637 39.4 0.1090 0.1092 0.1090
>
> Step 51, time 0.0102 (ps) LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.001802, max 0.029832 (between atoms 2026 and 2029)
> bonds that rotated more than 30 degrees:
> atom 1 atom 2 angle previous, current, constraint length
> 2331 2334 43.1 0.1090 0.1093 0.1090
> 2026 2028 49.6 0.1090 0.1095 0.1090
> 5071 5074 41.7 0.1090 0.1093 0.1090
> 4806 4808 47.0 0.1090 0.1095 0.1090
>
> Step 52, time 0.0104 (ps) LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.003002, max 0.049492 (between atoms 156 and 159)
> bonds that rotated more than 30 degrees:
> atom 1 atom 2 angle previous, current, constraint length
> 471 474 51.7 0.1090 0.1096 0.1090
> 2331 2334 32.4 0.1093 0.1078 0.1090
> 5071 5074 31.3 0.1093 0.1081 0.1090
> 156 160 55.3 0.1090 0.1095 0.1090
> 916 919 41.0 0.1090 0.1093 0.1090
> 5886 5890 61.1 0.1090 0.1092 0.1090
>
> Step 53, time 0.0106 (ps) LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.034606, max 0.843079 (between atoms 5886 and 5890)
> bonds that rotated more than 30 degrees:
> atom 1 atom 2 angle previous, current, constraint length
> 471 475 31.5 0.1049 0.1325 0.1090
> 471 474 92.9 0.1096 0.1519 0.1090
> 471 473 38.6 0.1044 0.1402 0.1090
> 471 472 92.7 0.1048 0.1568 0.1090
> 2331 2335 48.8 0.1082 0.1083 0.1090
> 2331 2334 48.4 0.1078 0.1070 0.1090
> 2331 2333 88.8 0.1110 0.1564 0.1090
> 2331 2332 88.8 0.1110 0.1586 0.1090
> 2026 2030 89.4 0.1103 0.1177 0.1090
> 2026 2028 40.0 0.1091 0.1191 0.1090
> 2026 2027 38.2 0.1089 0.1207 0.1090
> 5071 5075 41.9 0.1084 0.1048 0.1090
> 5071 5074 41.6 0.1081 0.1043 0.1090
> 5071 5073 88.6 0.1109 0.1376 0.1090
> 5071 5072 88.7 0.1110 0.1392 0.1090
> 4806 4810 89.3 0.1104 0.1176 0.1090
> 4806 4809 32.7 0.1104 0.0927 0.1090
> 4806 4808 35.2 0.1089 0.1140 0.1090
> 4806 4807 35.0 0.1088 0.1153 0.1090
> 156 160 92.7 0.1095 0.1324 0.1090
> 156 159 80.8 0.1036 0.0523 0.1090
> 156 158 90.0 0.1036 0.1338 0.1090
> 156 157 90.4 0.1037 0.1489 0.1090
> 2276 2280 38.3 0.1091 0.1114 0.1090
> 2276 2277 33.0 0.1089 0.1134 0.1090
> 2286 2290 37.8 0.1090 0.1102 0.1090
> 916 920 90.1 0.1068 0.1704 0.1090
> 916 919 45.9 0.1093 0.1237 0.1090
> 916 917 65.0 0.1067 0.1285 0.1090
> 1296 1300 31.2 0.1090 0.1094 0.1090
> 5886 5890 90.9 0.1092 0.2009 0.1090
> 5886 5889 47.9 0.1043 0.1326 0.1090
> 5886 5888 85.9 0.1045 0.1282 0.1090
> 5886 5887 91.4 0.1046 0.1208 0.1090
>
> Back Off! I just backed up step53b_n0.pdb to ./#step53b_n0.pdb.1#
>
> Back Off! I just backed up step53c_n0.pdb to ./#step53c_n0.pdb.1#
> Wrote pdb files with previous and current coordinates
> ..
> ..
> ..
>
> This is my .mdp file:
> title = Yo
> cpp = /usr/bin/cpp
> include =
> define =
>
> ; RUN CONTROL PARAMETERS
> integrator = steep
> ; Start time and timestep in ps
> tinit = 0
> dt = 0.0002
> nsteps = 1000
> ; For exact run continuation or redoing part of a run
> init_step = 0
> ; mode for center of mass motion removal
> comm_mode = Linear
> ; number of steps for center of mass motion removal
> nstcomm = 10
> ; ENERGY MINIMIZATION OPTIONS
> ; Force tolerance and initial step-size
> emtol = 0.0001
Note that you will never achieve this value with single precision (or likely
ever, for that matter).
> emstep = 0.00001
Something doesn't gel here. The step size indicated in the mdrun output above
suggests that your emstep is much larger than this value. Note that dt is not
used in conjunction with EM algorithms.
> ; Max number of iterations in relax_shells
> niter = 100
> ; Step size (ps^2) for minimization of flexible constraints
> fcstep = 0
> ; Frequency of steepest descents steps when doing CG
> nstcgsteep = 1000
> nbfgscorr = 10
>
> ; OUTPUT CONTROL OPTIONS
> ; Output frequency for coords (x), velocities (v) and forces (f)
> nstxout = 1
> nstvout = 100
> nstfout = 100
> nstcalcenergy = -1
> ; Checkpointing helps you continue after crashes
> nstcheckpoint = 1000
> ; Output frequency for energies to log file and energy file
> nstlog = 250
> nstenergy = 60
> ; Output frequency and precision for xtc file
> nstxtcout = 1
> xtc_precision = 1000
> ; This selects the subset of atoms for the xtc file. You can
> ; select multiple groups. By default all atoms will be written.
> xtc_grps =
> ; NEIGHBORSEARCHING PARAMETERS
> ; nblist update frequency
> nstlist = 20
nstlist should always be set to 1 for EM.
> ; ns algorithm (simple or grid)
> ns_type = grid
> ; Periodic boundary conditions: xyz (default), no (vacuum)
> ; or full (infinite systems only)
> pbc = xyz
> ; nblist cut-off
> rlist = 0.35
> rlistlong = 0.35 ; cut off distance for
These cutoff settings make no sense.
> short range neighbor list
> ; OPTIONS FOR ELECTROSTATICS AND VDW
> ; Method for doing electrostatics
> coulombtype = PME
> rcoulomb_switch = 0
> rcoulomb = 0.35
Same comment here regarding rcoulomb. You can't just choose arbitrary values
for these settings and hope they work. Force fields require certain cutoff
values. If you don't know them, spend some time reading about your chosen force
field - it will save you a lot of time and wasted data in the future.
> ; Method for doing Van der Waals
> vdw_type = Cut-off
> ; cut-off lengths
> rvdw_switch = 0
> rvdw = 0.35
Same comment regarding rvdw.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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