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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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==================================================
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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
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