Hi,
protein have 2 positive chage, I use PRODRG built .gro of CH3C00H, and add
two molecular CH3C00H, four molecular NA into system.
At energy minimization step, after steep, when I use cg, Fatal error:
DD cell 1 4 0 could only obtain 14 of the 16 atoms that are connected via
constraints from the neighboring cells. This probably means your constraint
lengths are too long compared to the domain decomposition cell size.
Decrease the number of domain decomposition grid cells or lincs-order.
I search the ways to sovle it in the GMX forum, there are some similar error
exist, I also try as the answers suggest, but I can not fix it. I don't
known what the cause.
things should go on....I want to do enery minimization more better in order
to avoid protein crash during simulation.
So, I try another way to do energ minimization. After steep, I use I-bfgs
steep .mdp:
title = bovin
cpp = /usr/bin/cpp
define = -DFLEXIBLE
constraints = all-bonds
integrator = cg
dt = 0.002 ; ps !
nsteps = 1000
nstlist = 10
ns_type = grid
rlist = 1.0
coulombtype = PME
rcoulomb = 1.0
vdwtype = cut-off
rvdw = 1.4
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
ewald_rtol = 1e-5
optimize_fft = yes
emtol = 100.0
emstep = 0.01
; GENERATE VELOCITIES FOR STARTUP RUN
gen-vel = no
gen-temp = 293
gen-seed = 173529
process:
Steepest Descents:
Tolerance (Fmax) = 1.00000e+03
Number of steps = 2000
Step= 0, Dmax= 1.0e-02 nm, Epot= -3.49891e+05 Fmax= 2.19267e+04, atom=
21003
Step= 1, Dmax= 1.0e-02 nm, Epot= -3.66773e+05 Fmax= 1.02238e+04, atom=
3054
Step= 2, Dmax= 1.2e-02 nm, Epot= -3.86198e+05 Fmax= 5.97878e+03, atom=
1146
Step= 3, Dmax= 1.4e-02 nm, Epot= -4.03308e+05 Fmax= 3.61163e+03, atom=
1146
Step= 4, Dmax= 1.7e-02 nm, Epot= -4.19782e+05 Fmax= 1.80657e+03, atom=
29071
Step= 5, Dmax= 2.1e-02 nm, Epot= -4.38870e+05 Fmax= 1.43308e+03, atom=
29071
Step= 6, Dmax= 2.5e-02 nm, Epot= -4.53627e+05 Fmax= 3.63104e+03, atom=
923
Step= 7, Dmax= 3.0e-02 nm, Epot= -4.58169e+05 Fmax= 4.16424e+03, atom=
923
Step 8, time 0.016 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.004145, max 0.106308 (between atoms 923 and 924)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
921 923 32.4 0.1385 0.1445 0.1340
923 927 33.0 0.1382 0.1444 0.1340
923 924 39.9 0.1386 0.1482 0.1340
924 925 34.2 0.1014 0.1068 0.1000
Step= 8, Dmax= 3.6e-02 nm, Epot= -4.60414e+05 Fmax= 5.82027e+03, atom= 31
Step 9, time 0.018 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.008160, max 0.128456 (between atoms 34 and 38)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
38 40 38.9 0.1410 0.1558 0.1390
34 38 39.9 0.1412 0.1569 0.1390
31 34 39.4 0.1414 0.1559 0.1390
31 32 38.6 0.1413 0.1545 0.1390
32 36 38.3 0.1412 0.1551 0.1390
36 40 38.2 0.1409 0.1552 0.1390
1020 1021 30.0 0.1397 0.1475 0.1390
1106 1110 32.9 0.1400 0.1499 0.1390
1103 1106 32.8 0.1401 0.1492 0.1390
1103 1104 32.1 0.1401 0.1488 0.1390
1104 1108 32.7 0.1400 0.1497 0.1390
1110 1112 32.4 0.1400 0.1496 0.1390
1108 1112 32.8 0.1400 0.1499 0.1390
Step 9, time 0.018 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.003367, max 0.128456 (between atoms 34 and 38)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
34 38 39.9 0.1412 0.1569 0.1390
38 40 38.9 0.1410 0.1558 0.1390
36 40 38.2 0.1409 0.1552 0.1390
32 36 38.3 0.1412 0.1551 0.1390
31 32 38.6 0.1413 0.1545 0.1390
31 34 39.4 0.1414 0.1559 0.1390
Step 9, time 0.018 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.008437, max 0.134299 (between atoms 373 and 377)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
368 371 39.6 0.1451 0.1559 0.1390
368 369 39.7 0.1452 0.1565 0.1390
369 373 41.3 0.1446 0.1576 0.1390
371 375 40.6 0.1446 0.1566 0.1390
373 377 42.3 0.1433 0.1577 0.1390
375 377 41.7 0.1432 0.1572 0.1390
921 923 31.5 0.1445 0.1442 0.1340
923 927 31.4 0.1444 0.1447 0.1340
923 924 42.0 0.1482 0.1496 0.1340
924 926 36.9 0.1065 0.1080 0.1000
924 925 37.3 0.1068 0.1082 0.1000
Step 9, time 0.018 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.004632, max 0.116116 (between atoms 923 and 924)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
921 923 31.5 0.1445 0.1442 0.1340
923 927 31.4 0.1444 0.1447 0.1340
923 924 42.0 0.1482 0.1496 0.1340
924 926 36.9 0.1065 0.1080 0.1000
924 925 37.3 0.1068 0.1082 0.1000
Step= 10, Dmax= 2.1e-02 nm, Epot= -4.63786e+05 Fmax= 3.33273e+03, atom=
1112
Step= 12, Dmax= 1.3e-02 nm, Epot= -4.65368e+05 Fmax= 3.16597e+03, atom=
518
Step= 13, Dmax= 1.5e-02 nm, Epot= -4.66743e+05 Fmax= 4.18187e+03, atom=
1112
Step= 14, Dmax= 1.9e-02 nm, Epot= -4.68028e+05 Fmax= 4.61798e+03, atom=
518
Step= 15, Dmax= 2.2e-02 nm, Epot= -4.68799e+05 Fmax= 5.19261e+03, atom=
522
Step= 16, Dmax= 2.7e-02 nm, Epot= -4.68896e+05 Fmax= 5.79535e+03, atom=
518
Step= 18, Dmax= 1.6e-02 nm, Epot= -4.72864e+05 Fmax= 1.66650e+03, atom=
522
Step= 19, Dmax= 1.9e-02 nm, Epot= -4.72901e+05 Fmax= 5.83070e+03, atom=
584
Step= 20, Dmax= 2.3e-02 nm, Epot= -4.75581e+05 Fmax= 4.25066e+03, atom=
160
Step= 22, Dmax= 1.4e-02 nm, Epot= -4.77224e+05 Fmax= 3.08540e+03, atom=
160
Step= 24, Dmax= 8.3e-03 nm, Epot= -4.78336e+05 Fmax= 1.29199e+03, atom=
160
Step= 25, Dmax= 1.0e-02 nm, Epot= -4.79314e+05 Fmax= 3.73890e+03, atom=
160
Step= 26, Dmax= 1.2e-02 nm, Epot= -4.80459e+05 Fmax= 2.21770e+03, atom=
160
Step= 27, Dmax= 1.4e-02 nm, Epot= -4.80600e+05 Fmax= 4.68351e+03, atom=
160
Step= 28, Dmax= 1.7e-02 nm, Epot= -4.81834e+05 Fmax= 3.60914e+03, atom=
160
Step= 30, Dmax= 1.0e-02 nm, Epot= -4.82982e+05 Fmax= 1.80313e+03, atom=
160
Step= 31, Dmax= 1.2e-02 nm, Epot= -4.83315e+05 Fmax= 4.15172e+03, atom=
160
Step= 32, Dmax= 1.5e-02 nm, Epot= -4.84337e+05 Fmax= 3.19667e+03, atom=
160
Step= 34, Dmax= 8.9e-03 nm, Epot= -4.85244e+05 Fmax= 1.44565e+03, atom=
160
Step= 35, Dmax= 1.1e-02 nm, Epot= -4.85711e+05 Fmax= 3.89936e+03, atom=
160
Step= 36, Dmax= 1.3e-02 nm, Epot= -4.86652e+05 Fmax= 2.48984e+03, atom=
160
Step= 38, Dmax= 7.7e-03 nm, Epot= -4.87292e+05 Fmax= 1.57431e+03, atom=
160
Step= 39, Dmax= 9.3e-03 nm, Epot= -4.87783e+05 Fmax= 3.04757e+03, atom=
160
Step= 40, Dmax= 1.1e-02 nm, Epot= -4.88394e+05 Fmax= 2.62054e+03, atom=
160
Step= 41, Dmax= 1.3e-02 nm, Epot= -4.88589e+05 Fmax= 3.92708e+03, atom=
160
Step= 42, Dmax= 1.6e-02 nm, Epot= -4.89062e+05 Fmax= 3.94266e+03, atom=
160
Step= 44, Dmax= 9.6e-03 nm, Epot= -4.90116e+05 Fmax= 9.30801e+02, atom=
160
writing lowest energy coordinates.
Back Off! I just backed up em.gro to ./#em.gro.1#
result:
Steepest Descents converged to Fmax < 1000 in 45 steps
Potential Energy = -4.9011588e+05
Maximum force = 9.3080109e+02 on atom 160
Norm of force = 7.3772133e+01
then I do I-bfgs,
Low-Memory BFGS Minimizer converged to machine precision in 175 steps,
but did not reach the requested Fmax < 100.
Potential Energy = -5.38089209528220e+05
Maximum force = 1.94381568185624e+06 on atom 10842
Norm of force = 1.61130387384634e+04
I chang emstep=0.005, result also not chang.
the .mdp is
title = bovin
cpp = /usr/bin/cpp ; the c pre-processor
define = -DFLEXIBLE
constraints = all-bonds
integrator = l-bfgs
dt = 0.002 ; ps !
nsteps = 2000
nstlist = 1
ns_type = grid
rlist = 1.0
coulombtype = PME
rcoulomb = 1.0
vdwtype = cut-off
rvdw = 1.4
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
ewald_rtol = 1e-5
optimize_fft = yes
;
; Energy minimizing stuff
;
emtol = 100.0
emstep =0.005
; GENERATE VELOCITIES FOR STARTUP RUN
gen-vel = no
gen-temp = 293
gen-seed = 173529
So, I have the question that why for cg, it take place fatal error? and
another question for steep, if the result is reasonable?
Thank you very much!
maggin
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