[gmx-users] gromacs error
Justin Lemkul
jalemkul at vt.edu
Thu Jul 31 14:19:20 CEST 2014
On 7/31/14, 8:16 AM, Urszula Uciechowska wrote:
> How should I correct the input file?
>
http://manual.gromacs.org/online/mdp_opt.html#vel
And get your hands on some suitable tutorial material; proper use of these
settings is routine.
-Justin
> Urszula Uciechowska
>>
>>
>> On 7/31/14, 7:42 AM, Urszula Uciechowska wrote:
>>> Dear Gromacs users,
>>>
>>>
>>> I tried to run coarse grained MD however after a few steps I got:
>>> Step 39, time 0.78 (ps) LINCS WARNING
>>> relative constraint deviation after LINCS:
>>> rms 0.038933, max 2.260527 (between atoms 10459 and 10463)
>>> bonds that rotated more than 30 degrees:
>>> atom 1 atom 2 angle previous, current, constraint length
>>> 10457 10459 89.8 0.3107 0.8288 0.3100
>>> 10459 10463 90.3 0.3075 1.0108 0.3100
>>> 10463 10467 90.6 0.3084 0.8774 0.3100
>>> 10467 10469 81.1 0.3103 0.3823 0.3100
>>> 10469 10471 90.3 0.3121 0.1885 0.3100
>>> Wrote pdb files with previous and current coordinates
>>>
>>> Step 40, time 0.8 (ps) LINCS WARNING
>>> relative constraint deviation after LINCS:
>>> rms 165002.767686, max 10334958.000000 (between atoms 10457 and 10459)
>>> bonds that rotated more than 30 degrees:
>>> atom 1 atom 2 angle previous, current, constraint length
>>> 10443 10445 30.1 0.3100 0.3581 0.3100
>>> 10445 10447 102.2 0.3102 266.6146 0.3100
>>> 10447 10450 59.3 0.3100 624.1382 0.3100
>>> 10450 10452 101.4 0.3105 5390.4609 0.3100
>>> 10452 10454 87.9 0.3083 104154.3047 0.3100
>>> 10454 10457 83.9 0.3497 439143.5312 0.3100
>>> 10457 10459 87.5 0.8288 3203837.2500 0.3100
>>> 10459 10463 87.8 1.0108 2960821.2500 0.3100
>>> 10463 10467 95.2 0.8774 763857.8125 0.3100
>>> 10467 10469 95.5 0.3823 195859.2656 0.3100
>>> 10469 10471 104.3 0.1885 43565.4141 0.3100
>>> 10471 10473 90.3 0.3534 7857.3394 0.3100
>>> 10473 10475 105.5 0.3125 57.7529 0.3100
>>> 10475 10477 90.0 0.3099 0.3849 0.3100
>>> 10477 10480 32.4 0.3101 0.3647 0.3100
>>> Wrote pdb files with previous and current coordinates
>>> mpiexec: process_obit_event: evt 6 task 0 on wn518 stat 267.
>>> mpiexec: wait_tasks: waiting for wn350 wn350 wn501.
>>> mpiexec: kill_others_now: alarm went off, killing all other tasks.
>>> mpiexec: kill_tasks: killing all tasks.
>>> mpiexec: process_kill_event: evt 10 task 1 on wn350.
>>> mpiexec: process_kill_event: evt 12 task 3 on wn501.
>>> mpiexec: process_kill_event: evt 11 task 2 on wn350.
>>> mpiexec: process_obit_event: evt 7 task 3 on wn501 stat 265.
>>> mpiexec: process_obit_event: evt 8 task 1 on wn350 stat 265.
>>> mpiexec: process_obit_event: evt 9 task 2 on wn350 stat 265.
>>> mpiexec: Warning: task 0 died with signal 11 (Segmentation fault).
>>> mpiexec: Warning: tasks 1-3 died with signal 9 (Killed).
>>>
>>> in log file last line is:
>>>
>>> Constraining the starting coordinates (step 0)
>>>
>>> Constraining the coordinates at t0-dt (step 0)
>>> RMS relative constraint deviation after constraining: 4.04e-06
>>> Initial temperature: 1.8161e-07 K
>>>
>>> Started mdrun on node 0 Wed Jul 30 10:39:50 2014
>>>
>>> Step Time Lambda
>>> 0 0.00000 0.00000
>>>
>>> Grid: 42 x 42 x 42 cells
>>> Energies (kJ/mol)
>>> Bond G96Angle Proper Dih. Improper Dih. LJ
>>> (SR)
>>> 6.24872e+03 1.47844e+04 1.75778e+03 4.11810e+02
>>> -2.32179e+07
>>> Coulomb (SR) Position Rest. Potential Kinetic En. Total
>>> Energy
>>> -4.49776e+03 2.00073e-01 -2.31992e+07 1.44043e+01
>>> -2.31992e+07
>>> Temperature Pressure (bar) Constr. rmsd
>>> 1.55259e-03 -1.41563e+03 5.56533e-06
>>>
>>> my input file:
>>>
>>> define = -DPOSRES
>>> dt = 0.02
>>> nsteps = 25000
>>> nstxout = 0
>>> nstvout = 0
>>> nstlog = 100
>>> nstxtcout = 100
>>> xtc-precision = 10
>>> rlist = 1.4
>>> coulombtype = shift
>>> rcoulomb = 1.2
>>> epsilon_r = 15
>>> vdw-type = shift
>>> rvdw-switch = 0.9
>>> rvdw = 1.2
>>> tcoupl = v-rescale
>>> tc-grps = Protein W
>>> tau-t = 1.0 1.0
>>> ref-t = 300 300
>>> Pcoupl = Berendsen
>>> Pcoupltype = isotropic
>>> tau-p = 12.0
>>> compressibility = 3e-4
>>> ref-p = 1.0
>>> refcoord_scaling = com
>>>
>>> What is wrong here?
>>>
>>
>> Likely this:
>>
>> Initial temperature: 1.8161e-07 K
>>
>> You haven't generated any velocities, so your system is effectively
>> frozen, and
>> you're simultaneously applying a thermostat and barostat, which probably
>> cause
>> your velocities to go absolutely insane, blowing up the system.
>>
>> Generate velocities at the desired temperature and equilibrate gently.
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 601
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>>
>> ==================================================
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>
>
>
> -----------------------------------------
> Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego
> http://www.ug.edu.pl/
>
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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