[gmx-users] Error during npt equilibration in coarse grained simulation

[Justin Lemkul]

On 2/25/13 12:16 AM, Anu Chandran wrote:
> Dear users,
> I am trying to do a coarse grained simulation of an octamer of a 350
> residue protein in water using gromacs-4.5.3 using martini force field. I
> got the following error when i started running NPT equilibration
>
> "Step 32, time 0.64 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 16.561310, max 137.568573 (between atoms 626 and 627)
> bonds that rotated more than 30 degrees:
>   atom 1 atom 2  angle  previous, current, constraint length
>
> Step 32, time 0.64 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 438.087891, max 3717.233887 (between atoms 580 and 581)
> bonds that rotated more than 30 degrees:
>   atom 1 atom 2  angle  previous, current, constraint length
>      626    627  121.9    0.2705  36.7207      0.2650
>      621    622   90.0    0.2756   0.4600      0.2700
>      624    626   91.5    0.3368 269.7515      0.3300
>      621    623   90.0    0.2756   0.3172      0.2700
>      620    624   90.4    0.3164 432.6003      0.3100
>      622    623   90.0    0.2756   0.3991      0.2700
>      618    620   85.5    0.3164 477.1006      0.3100
>      626    627  121.9    0.2705  36.7206      0.2650
>      615    618   88.6    0.3164 211.2461      0.3100
>      607    610  141.3    0.3164  14.3253      0.3100
>
> Step 32, time 0.64 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 134.347206, max 2000.691284 (between atoms 4949 and 4946)
> bonds that rotated more than 30 degrees:
>   atom 1 atom 2  angle  previous, current, constraint length
>      610    612  149.2    0.3164  17.6610      0.3100
>      612    614   89.7    0.3164   3.1394      0.3100
>      614    615  150.9    0.3164   9.9306      0.3100
>      615    618   88.6    0.3164 211.1131      0.3100
>      618    620   85.5    0.3164 477.0737      0.3100
>      620    624   90.4    0.3164 432.5994      0.3100
>     4950   4949   75.8    0.3164 146.5132      0.3100
>      624    626   91.5    0.3368 269.7514      0.3300
>     4952   4950  118.9    0.3164  14.6303      0.3100
>      468    469   90.0    0.2705  24.6834      0.2650
>     4941   4939   90.0    0.3368   8.5601      0.3300
>      585    586   61.3    0.2756   0.3361      0.2700
>     4944   4941   82.5    0.3164 206.9830      0.3100
>      586    587   90.1    0.2756   0.3137      0.2700
>     4946   4944   90.0    0.3164 583.5660      0.3100
>      606    607   90.0    0.3368   6.6314      0.3300
>     4949   4946   90.0    0.3164 620.5243      0.3100
>      580    581   91.9    0.4030 1003.9232      0.2700
>     4954   4952   90.3    0.3164   1.6571      0.3100
>      580    582   89.8    0.2756 960.9988      0.2700
>      582    583   98.6    0.2756 592.0677      0.2700
>      463    464   90.0    0.2654   7.6858      0.2600
>      581    582   88.8    0.1280 193.0707      0.2700
>      581    583   91.3    0.2254 514.1149      0.2700
> Wrote pdb files with previous and current coordinates
> Wrote pdb files with previous and current coordinates
> Segmentation fault (core dumped)"
>
>
> Energy minimization and the NVT equilibration ran without any error or
> warning. The mdp file used is as shown below;
>
> title                    = Martini
> define                   = -DPOSRES
> integrator               = md
> dt                       = 0.02
> nsteps                   = 50000
> nstcomm                  = 10
> comm-grps                =
> nstxout                  = 0
> nstvout                  = 0
> nstfout                  = 0
> nstlog                   = 1000
> nstenergy                = 100
> nstxtcout                = 1000
> xtc_precision            = 100
> xtc-grps                 =
> energygrps               = Protein W
> nstlist                  = 10
> ns_type                  = grid
> pbc                      = xyz
> rlist                    = 1.4
> coulombtype              = Shift
> rcoulomb_switch          = 0.0
> rcoulomb                 = 1.2
> epsilon_r                = 15
> vdw_type                 = Shift
> rvdw_switch              = 0.9
> rvdw                     = 1.2
> tcoupl                   = v-rescale
> tc-grps                  = System
> tau_t                    = 1.0
> ref_t                    = 300
> Pcoupl                   = parrinello-rahman
> Pcoupltype               = isotropic
> tau_p                    = 5.0
> compressibility          = 3e-4
> ref_p                    = 1.0
> gen_vel                  = yes

If you ran NVT previously, regenerating velocities defeats that purpose and 
perturbs the system unnecessarily.  Further, Parrinello-Rahman is not very 
stable for initial equilibration; use Berendsen and then switch to P-R for data 
collection.

> gen_temp                 = 300
> gen_seed                 = 473529
> constraints              = none
> constraint_algorithm     = Lincs
> unconstrained_start      = no
> lincs_order              = 4
> lincs_warnangle          = 30
>
> Also the water box after energy minimization showed some gaps towards the
> edge of the box when visualized using VMD.
>
>
> can anybody please help me on how to overcome this error?
>

In addition to the above, see the standard advice for unstable systems:

http://www.gromacs.org/Documentation/Terminology/Blowing_Up

-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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