Dear Justin,
i am trying to insert a peptide in trans-bialyer orientation
into a pre-equilibrated POPC bilayer using inflategro script. After 13 steps
of compression, the area per lipid is 2.61956768363491 nm^2, whereas the
desired area per lipid is 0.658 nm^2. But when i try to energy minimize the
compressed structure after 13th steps of compression, the energy did not
converged and give the following errors. During em i use strong position
restraints on peptide heavy atom using force constants of 100000.
------------------------------
perl inflategro em_13.gro 0.95 POPC 0 com_13.gro 5 area_lip.dat
grompp -f enermin.mdp -c com_13.gro -p system.top -o em_14.tpr
mdrun -s em_14.tpr -nice 4 -o em_14 -c em_14 -e em_14 -g em_14&
Reading file em_14.tpr, VERSION 3.3.1 (single precision)
Steepest Descents:
Tolerance (Fmax) = 1.00000e+03
Number of steps = 50000
Step 9, time 0.018 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max 0.001381 (between atoms 72 and 74) rms 0.000054
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
539 540 35.7 0.1000 0.1000 0.1000
Step 15, time 0.03 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max 0.003842 (between atoms 65 and 68) rms 0.000141
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
539 540 38.3 0.1000 0.1000 0.1000
Step 16, time 0.032 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max 0.016511 (between atoms 65 and 68) rms 0.000550
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
65 66 42.8 0.1390 0.1412 0.1390
65 68 42.9 0.1390 0.1413 0.1390
66 70 41.9 0.1390 0.1411 0.1390
68 72 41.1 0.1390 0.1411 0.1390
70 74 39.6 0.1390 0.1407 0.1390
72 74 38.7 0.1390 0.1406 0.1390
344 345 34.8 0.1390 0.1397 0.1390
344 347 34.4 0.1390 0.1397 0.1390
345 349 33.6 0.1390 0.1397 0.1390
347 351 33.1 0.1390 0.1397 0.1390
349 353 32.7 0.1390 0.1397 0.1390
351 353 32.6 0.1390 0.1397 0.1390
381 382 33.3 0.1390 0.1396 0.1390
381 384 33.5 0.1390 0.1396 0.1390
382 386 32.9 0.1390 0.1396 0.1390
384 388 33.2 0.1390 0.1396 0.1390
386 390 32.4 0.1390 0.1396 0.1390
388 390 32.5 0.1390 0.1396 0.1390
539 540 49.3 0.1000 0.1000 0.1000
546 547 33.5 0.1250 0.1250 0.1250
Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 1000
Double precision normally gives you higher accuracy.
You might need to increase your constraint accuracy, or turn
off constraints alltogether (set constraints = none in mdp file)
writing lowest energy coordinates.
Steepest Descents converged to machine precision in 43 steps,
but did not reach the requested Fmax < 1000.
Potential Energy = -1.2865473e+05
Maximum force = 4.7082656e+04 on atom 547
Norm of force = 6.7057188e+04
gcq#38: "I'm Your Worst Nightmare" (Creep)
-------------------------------------------------------------------------
my enermin.mdp file is .......................
-------------------------------------------------
title = sp position restraining
cpp = /usr/bin/cpp
define = -DPOSRES
constraints = all-bonds
constraint_algorithm= lincs
lincs_order = 4
lincs_iter = 6
lincs_warnangle = 30
integrator = steep ; Algorithm (steep = steepest descent
minimization)
dt = 0.002 ; ps !
nsteps = 50000 ; Maximum number of (minimization) steps to
perform
nstlog = 200
nstlist = 1
ns_type = grid
rlist = 1.2 ; Cut-off for making neighbor list (short range
forces)
rcoulomb = 1.2
rvdw = 1.2
coulombtype = PME
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
ewald_rtol = 1e-5
optimize_fft = yes
pbc = xyz ; Periodic Boundary Conditions (yes/no)
;
; Energy minimizing stuff
;
emtol = 1000
emstep = 0.01
---------------
should i continue further compression with this energy minimized structure
(em_14.gro)??
if not how can i slove this problem.
waiting for ur suggestion.
Moutusi Manna
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