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
-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
========================================
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