[gmx-users] Error during npt equilibration in coarse grained simulation
Justin Lemkul
jalemkul at vt.edu
Tue Feb 26 12:53:34 CET 2013
On 2/26/13 12:51 AM, Anu Chandran wrote:
> Sir,
> I have tried Berendsen barostat for Pcoupl. Still I get the same error.
>
So have a look at the other recommendations on the page I linked. Thermostat
instability is just one possibility. We have had numerous reports, just in the
last week, of crashes with CG force fields during equilibration (hint: check the
archives). You probably need either better minimization or a shorter time step.
-Justin
> 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>
>>
>> ==============================**==========
>> --
>> gmx-users mailing list gmx-users at gromacs.org
>> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
>> * Please search the archive at http://www.gromacs.org/**
>> Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
>> * Please don't post (un)subscribe requests to the list. Use the www
>> interface or send it to gmx-users-request at gromacs.org.
>> * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>>
--
========================================
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
========================================
More information about the gromacs.org_gmx-users
mailing list