[gmx-users] Error during npt equilibration in coarse grained simulation
Anu Chandran
miscofanu at gmail.com
Tue Feb 26 06:51:40 CET 2013
Sir,
I have tried Berendsen barostat for Pcoupl. Still I get the same error.
Thank you,
regards,
Anu
On Mon, Feb 25, 2013 at 6:58 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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<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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
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