[gmx-users] gromacs error
Urszula Uciechowska
urszula.uciechowska at biotech.ug.edu.pl
Thu Jul 31 14:16:37 CEST 2014
How should I correct the input file?
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
>
> ==================================================
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send
> a mail to gmx-users-request at gromacs.org.
>
>
-----------------------------------------
Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego
http://www.ug.edu.pl/
More information about the gromacs.org_gmx-users
mailing list