Thank you Berk,
I will loon into tau_t=1.0 (or at least not = 0.1). Thank you for the hint.
These simulations run in 200 ps segments and utilize restarts via
grompp -t -e like this:
EXECUTING:
/hpf/projects1/pomes/cneale/exe/gromacs-4.0.3/exec/bin/grompp -f
/scratch/4772976.1.ompi-4-21.q/md6_running/dpc50_md6.mdp -c
md5_success/dpc50_md5.gro -p dpc50.top -n dpc50.ndx -o
/scratch/4772976.1.ompi-4-21.q/md6_running/dpc50_md6.tpr -maxwarn 1 -t
md5_success/dpc50_md5.trr -e md5_success/dpc50_md5.edr
The -maxwarn 1 is to avoid this message:
WARNING 1 [file
/scratch/4772976.1.ompi-4-21.q/md5_running/dpc50_md5.mdp, line unknown]:
Can not couple a molecule with free_energy = no
which I don't think should be a problem.
###
I didn't check temperatures previously, but I did check the energy
components output the the .log file in zero step mdruns in both serial
and parallel and found no difference.
Here is the information on temperature and total energy for the serial
and parallel runs:
For the run in parallel:
Last energy frame read 780 time 7800.000
Statistics over 1950001 steps [ 0.0000 thru 7800.0000 ps ], 1 data sets
All averages are exact over 1950001 steps
Energy Average RMSD Fluct. Drift
Tot-Drift
-------------------------------------------------------------------------------
Temperature 303.322 901.905 901.905 -6.34952e-06
-0.0495263
Heat Capacity Cv: -1.01712 J/mol K (factor = 8.84124)
## and a snippit from the energy.xvg file:
0.000000 315.837738
10.000000 301.955261
20.000000 301.284363
30.000002 301.899048
40.000000 303.823578
50.000004 303.616943
60.000004 304.325684
70.000000 303.450500
80.000000 303.068085
90.000008 306.214508
100.000008 304.300598
110.000008 299.399780
120.000008 303.130493
130.000000 303.316864
140.000000 303.161743
150.000000 302.372162
160.000000 301.881927
170.000015 304.809631
...
7700.000000 304.224426
7710.000000 301.240784
7720.000000 305.885162
7730.000000 302.651276
7740.000000 304.464722
7750.000000 303.531769
7760.000000 301.380066
7770.000000 301.940125
7780.000000 303.458893
7790.000000 303.814270
7800.000000 300.946259
####################
And from the serial run:
Last energy frame read 240 time 2400.000
Statistics over 600001 steps [ 0.0000 thru 2400.0000 ps ], 1 data sets
All averages are exact over 600001 steps
Energy Average RMSD Fluct. Drift
Tot-Drift
-------------------------------------------------------------------------------
Temperature 303.277 451.075 451.075 -0.000429073
-1.02978
Heat Capacity Cv: -5.37983 J/mol K (factor = 2.21216)
gcq#217: "Hey Man You Know, I'm Really OK" (Offspring)
## and a snippit from the energy.xvg file:
0.000000 316.556885
10.000000 304.426270
20.000000 304.430847
30.000002 302.170471
40.000000 302.507294
50.000004 306.278442
60.000004 301.382263
70.000000 303.833801
80.000000 302.321655
90.000008 301.548462
100.000008 300.902130
110.000008 307.839355
120.000008 302.419922
130.000000 301.922119
140.000000 303.287079
150.000000 303.745911
160.000000 301.719269
...
2320.000000 304.992310
2330.000000 301.203186
2340.000000 304.222290
2350.000000 301.157288
2360.000000 301.428009
2370.000000 304.554443
2380.000000 299.534973
2390.000000 301.980865
2400.000000 302.382721
########################
Then looking at total energy:
For the parallel run:
Last energy frame read 780 time 7800.000
Statistics over 1950001 steps [ 0.0000 thru 7800.0000 ps ], 1 data sets
All averages are exact over 1950001 steps
Energy Average RMSD Fluct. Drift
Tot-Drift
-------------------------------------------------------------------------------
Total Energy -279021 829645 829645 -0.0113049
-88.1784
gcq#281: "I'll Match Your DNA" (Red Hot Chili Peppers)
## And for the serial run:
Last energy frame read 240 time 2400.000
Statistics over 600001 steps [ 0.0000 thru 2400.0000 ps ], 1 data sets
All averages are exact over 600001 steps
Energy Average RMSD Fluct. Drift
Tot-Drift
-------------------------------------------------------------------------------
Total Energy -278924 414939 414939 0.0498045
119.531
gcq#323: "Your Shopping Techniques are Amazing" (Gogol Bordello)
##########
Since I used only one temperature coupling group for SD (which is
another obvious difference between the MD runs and SD runs and is
something that I am testing right now) I don't have separate
temperature information for detergents vs. water. What i can give you,
though is all of the averages/drifts from the serial and parallel
simulations:
### PARALLEL:
Statistics over 1950001 steps [ 0.0000 thru 7800.0000 ps ], 76 data sets
The terms 'Coul-14:SOL-SOL' 'LJ-14:SOL-SOL' 'Coul-14:SOL-DPC'
'LJ-14:SOL-DPC' 'Coul-14:SOL-DPN' 'LJ-14:SOL-DPN' 'Coul-14:DPC-DPN'
'LJ-14:DPC-DPN' are averaged over 781 frames
All other averages are exact over 1950001 steps
Energy Average RMSD Fluct. Drift
Tot-Drift
-------------------------------------------------------------------------------
Angle 2827.07 8406.19 8406.19 0.00113105
8.82218
Proper Dih. 675.162 2004.62 2004.62 0.00136083
10.6145
Ryckaert-Bell. 1021.92 3032.98 3032.98 0.000496043
3.86914
LJ-14 741.346 2201.26 2201.26 0.00101757
7.93706
Coulomb-14 6399.81 19057.6 19057.6 -0.00643754
-50.2129
LJ (SR) 49828 148169 148169 -0.00683079
-53.2802
LJ (LR) -1848.3 5495.7 5495.7 -9.92975e-05
-0.774521
Disper. corr. -636.214 1891.61 1891.61 -3.5155e-05
-0.274209
Coulomb (SR) -323920 963143 963143 -0.00590314
-46.0445
Coul. recip. -71392.8 212309 212309 0.00519419
40.5147
Potential -336304 999970 999970 -0.0101058
-78.8255
Kinetic En. 57282.9 170326 170326 -0.00119919
-9.35371
Total Energy -279021 829645 829645 -0.0113049
-88.1784
Temperature 303.322 901.905 901.905 -6.34952e-06
-0.0495263
Pressure (bar) 0.896599 142.893 142.872 -0.00109268
-8.52289
Cons. rmsd () -8.11414e-11 0 0 0
0
Cons.2 rmsd () -7.73233e-11 0 0 0
0
Box-X 7.19249 21.3864 21.3864 -1.32351e-07
-0.00103234
Box-Y 7.19249 21.3864 21.3864 -1.32351e-07
-0.00103234
Box-Z 4.68869 13.9415 13.9415 -8.64041e-08
-0.000673952
Volume 242.555 721.246 721.246 -1.33934e-05
-0.104469
Density (SI) 1005.85 2990.62 2990.62 5.55743e-05
0.43348
pV 13.0787 2087.48 2087.17 -0.016043
-125.135
Vir-XX 19071.5 56716.6 56716.6 -0.00854941
-66.6854
Vir-XY 3.76437 996.264 995.712 -0.0147231
-114.84
Vir-XZ -8.26286 996.173 995.837 -0.0114991
-89.6933
Vir-YX 3.8099 995.544 994.943 -0.0153689
-119.877
Vir-YY 19083.8 56764.5 56764.5 0.00839835
65.5071
Vir-YZ -9.43815 994.226 993.533 -0.0164852
-128.584
Vir-ZX -8.24832 996.226 995.88 -0.0116533
-90.8961
Vir-ZY -9.44322 994.007 993.335 -0.0162358
-126.639
Vir-ZZ 19107.9 56848.2 56848.1 0.0230164
179.528
Pres-XX (bar) 2.51466 215.649 215.636 0.00104893
8.18168
Pres-XY (bar) -1.21277 138.446 138.398 0.00163452
12.7493
Pres-XZ (bar) 1.11071 137.965 137.939 0.00118269
9.22498
Pres-YX (bar) -1.21901 138.346 138.292 0.00172294
13.4389
Pres-YY (bar) 1.05221 216.336 216.299 -0.00177097
-13.8136
Pres-YZ (bar) 0.480955 137.679 137.572 0.00241359
18.826
Pres-ZX (bar) 1.10872 137.971 137.945 0.00120378
9.38951
Pres-ZY (bar) 0.48165 137.647 137.542 0.00237939
18.5593
Pres-ZZ (bar) -0.87707 210.218 210.14 -0.00255599
-19.9368
#Surf*SurfTen -12.4756 1117.28 1117.04 -0.0102882
-80.2483
Mu-X 25.2118 577.038 567.836 -0.0455856
-355.568
Mu-Y 452.298 1166.36 1156.35 0.067708
528.122
Mu-Z 228.086 782.637 781.802 -0.0160502
-125.192
Coul-SR:SOL-SOL -306676 911956 911956 0.017729
138.286
LJ-SR:SOL-SOL 53758.2 159865 159865 -0.011465
-89.4271
LJ-LR:SOL-SOL -1218.29 3622.34 3622.34 -3.60649e-05
-0.281306
Coul-14:SOL-SOL 0 0 0 0
0
LJ-14:SOL-SOL 0 0 0 0
0
Coul-SR:SOL-DPC -14967.6 44363.8 44363.8 -0.0378241
-295.028
LJ-SR:SOL-DPC -908.102 2694.55 2694.55 0.000250572
1.95446
LJ-LR:SOL-DPC -341.353 1013.98 1013.98 -0.00026287
-2.05039
Coul-14:SOL-DPC 0 0 0 0
0
LJ-14:SOL-DPC 0 0 0 0
0
Coul-SR:SOL-DPN -315.337 948.402 948.381 0.00276681
21.5811
LJ-SR:SOL-DPN -11.8356 44.3978 44.3215 0.00115573
9.01471
LJ-LR:SOL-DPN -6.47523 19.9746 19.971 0.000168898
1.31741
Coul-14:SOL-DPN 0 0 0 0
0
LJ-14:SOL-DPN 0 0 0 0
0
Coul-SR:DPC-DPC -1920.34 5760.84 5760.78 0.0122671
95.6836
LJ-SR:DPC-DPC -2897.64 8636.66 8636.66 0.00489904
38.2125
LJ-LR:DPC-DPC -270.101 804.597 804.597 0.000296762
2.31474
Coul-14:DPC-DPC 6273.7 18681.9 18681.9 -0.00621425
-48.4711
LJ-14:DPC-DPC 726.47 2157.22 2157.22 0.00100007
7.80055
Coul-SR:DPC-DPN -9.96564 27.4085 27.3184 -0.000986307
-7.6932
LJ-SR:DPC-DPN -99.3615 288.913 288.894 -0.0014542
-11.3428
LJ-LR:DPC-DPN -11.829 34.1307 34.1256 -0.000263447
-2.05489
Coul-14:DPC-DPN 0 0 0 0
0
LJ-14:DPC-DPN 0 0 0 0
0
Coul-SR:DPN-DPN -30.2965 91.3759 91.3753 0.00014471
1.12874
LJ-SR:DPN-DPN -13.2866 38.5078 38.5047 -0.000216818
-1.69118
LJ-LR:DPN-DPN -0.253457 0.740982 0.740959 -2.57124e-06
-0.0200557
Coul-14:DPN-DPN 126.114 375.996 375.996 -0.00022329
-1.74166
LJ-14:DPN-DPN 14.8763 44.2678 44.2678 1.75021e-05
0.136516
T-System 303.322 901.905 901.905 -6.34952e-06
-0.0495263
Heat Capacity Cv: -1.01712 J/mol K (factor = 8.84124)
Isothermal Compressibility: 51.2113 /bar
Adiabatic bulk modulus: 0.0195269 bar
### SERIAL:
Last energy frame read 240 time 2400.000
Statistics over 600001 steps [ 0.0000 thru 2400.0000 ps ], 76 data sets
The terms 'Coul-14:SOL-SOL' 'LJ-14:SOL-SOL' 'Coul-14:SOL-DPC'
'LJ-14:SOL-DPC' 'Coul-14:SOL-DPN' 'LJ-14:SOL-DPN' 'Coul-14:DPC-DPN'
'LJ-14:DPC-DPN' are averaged over 241 frames
All other averages are exact over 600001 steps
Energy Average RMSD Fluct. Drift
Tot-Drift
-------------------------------------------------------------------------------
Angle 2830.23 4221.38 4221.37 0.00960858
23.0606
Proper Dih. 680.513 1015.9 1015.89 -0.00175867
-4.22082
Ryckaert-Bell. 1014.28 1503.1 1503.09 0.00613028
14.7127
LJ-14 739.002 1101.4 1101.4 -0.00091984
-2.20762
Coulomb-14 6390.08 9525.68 9525.63 -0.0447155
-107.317
LJ (SR) 49733.3 74008.9 74008.9 -0.0340118
-81.6285
LJ (LR) -1843.61 2744.46 2744.46 0.0031249
7.49976
Disper. corr. -636.29 946.31 946.31 -0.000111216
-0.266919
Coulomb (SR) -323770 481666 481666 0.149312
358.349
Coul. recip. -71335.4 106138 106138 0.0441727
106.015
Potential -336198 500125 500125 0.130836
314.006
Kinetic En. 57274.4 85186.2 85186.2 -0.0810311
-194.475
Total Energy -278924 414939 414939 0.0498045
119.531
Temperature 303.277 451.075 451.075 -0.000429073
-1.02978
Pressure (bar) 0.961481 144.598 144.333 0.0126134
30.2721
Cons. rmsd () -7.3231e-11 0 0 0
0
Cons.2 rmsd () -6.9743e-11 0 0 0
0
Box-X 7.19221 10.6977 10.6977 -4.19267e-07
-0.00100624
Box-Y 7.19221 10.6977 10.6977 -4.19267e-07
-0.00100624
Box-Z 4.6885 6.97371 6.97371 -2.73206e-07
-0.000655696
Volume 242.526 360.757 360.757 -4.24149e-05
-0.101796
Density (SI) 1005.97 1496.11 1496.11 0.000175845
0.422029
pV 14.0243 2111.91 2108.06 0.184157
441.977
Vir-XX 19091.6 28413.8 28413.7 0.138935
333.444
Vir-XY -29.2057 997.698 997.46 0.0314206
75.4096
Vir-XZ 3.92948 994.406 994.121 -0.0343281
-82.3877
Vir-YX -29.2209 997.709 997.476 0.0311268
74.7044
Vir-YY 19055.4 28395.8 28395.4 -0.233472
-560.333
Vir-YZ -23.6583 993.885 993.404 -0.044622
-107.093
Vir-ZX 3.93959 994.396 994.098 -0.0351758
-84.4221
Vir-ZY -23.6524 993.86 993.355 -0.0457267
-109.744
Vir-ZZ 19106.4 28472.3 28471.7 -0.262729
-630.552
Pres-XX (bar) -0.886528 215.952 215.32 -0.0238309
-57.1943
Pres-XY (bar) 3.74481 138.257 138.24 -0.00305744
-7.33787
Pres-XZ (bar) -1.27622 137.953 137.857 0.00742417
17.818
Pres-YX (bar) 3.7469 138.258 138.242 -0.00301706
-7.24096
Pres-YY (bar) 5.8636 213.786 212.888 0.0282522
67.8055
Pres-YZ (bar) 4.5372 137.856 137.838 0.00314296
7.54312
Pres-ZX (bar) -1.2776 137.952 137.853 0.00754041
18.097
Pres-ZY (bar) 4.5364 137.853 137.834 0.00329443
7.90665
Pres-ZZ (bar) -2.09262 215.114 213.864 0.0334187
80.2051
#Surf*SurfTen -21.4754 1121.19 1116.59 0.146315
351.157
Mu-X 227.757 833.196 779.584 -0.424421
-1018.61
Mu-Y 519.448 1040.48 1027.64 -0.235255
-564.613
Mu-Z 197.25 578.977 557.265 -0.226706
-544.096
Coul-SR:SOL-SOL -306056 455439 455439 0.326938
784.653
LJ-SR:SOL-SOL 53767.7 79955.9 79955.9 0.0255695
61.3668
LJ-LR:SOL-SOL -1206.49 1799.86 1799.85 0.00686592
16.4782
Coul-14:SOL-SOL 0 0 0 0
0
LJ-14:SOL-SOL 0 0 0 0
0
Coul-SR:SOL-DPC -15585.1 23051.3 23050.9 -0.193565
-464.557
LJ-SR:SOL-DPC -1276.41 1744.46 1738.91 -0.20058
-481.393
LJ-LR:SOL-DPC -379.445 547.206 546.982 -0.0225622
-54.1493
Coul-14:SOL-DPC 0 0 0 0
0
LJ-14:SOL-DPC 0 0 0 0
0
Coul-SR:SOL-DPN -278.743 390.78 390.091 -0.0334985
-80.3965
LJ-SR:SOL-DPN -16.3179 24.5521 23.73 -0.00909363
-21.8247
LJ-LR:SOL-DPN -6.91459 9.71059 9.69638 -0.000757895
-1.81895
Coul-14:SOL-DPN 0 0 0 0
0
LJ-14:SOL-DPN 0 0 0 0
0
Coul-SR:DPC-DPC -1798.53 2703.56 2703.44 0.0361755
86.8212
LJ-SR:DPC-DPC -2629.37 4014.47 4013.31 0.139122
333.894
LJ-LR:DPC-DPC -238.984 369.468 369.249 0.0183626
44.0704
Coul-14:DPC-DPC 6265.13 9332.28 9332.25 -0.0343079
-82.339
LJ-14:DPC-DPC 723.962 1079.51 1079.51 -0.00150033
-3.60079
Coul-SR:DPC-DPN -21.7104 39.9899 39.6634 0.0073602
17.6645
LJ-SR:DPC-DPN -99.4828 158.67 158.455 0.011905
28.572
LJ-LR:DPC-DPN -11.5257 18.0729 18.0527 0.00123404
2.96169
Coul-14:DPC-DPN 0 0 0 0
0
LJ-14:DPC-DPN 0 0 0 0
0
Coul-SR:DPN-DPN -30.1847 50.3626 50.1961 0.00590551
14.1732
LJ-SR:DPN-DPN -12.786 18.543 18.5317 -0.000935153
-2.24437
LJ-LR:DPN-DPN -0.251368 0.362826 0.362621 -1.76176e-05
-0.0422822
Coul-14:DPN-DPN 124.956 194.161 194.027 -0.0104076
-24.9784
LJ-14:DPN-DPN 15.04 22.3795 22.3759 0.000580485
1.39317
T-System 303.277 451.075 451.075 -0.000429073
-1.02978
Heat Capacity Cv: -5.37983 J/mol K (factor = 2.21216)
Isothermal Compressibility: 12.8158 /bar
Adiabatic bulk modulus: 0.0780289 bar
########
Note that all of the .edr information above is from many separately
generated 200 ps .edr files, which I first concatenated via eneconv
and then ran g_energy on the total .edr file. I am not sure if this
affects the overall averages/rmsd values or not.
Thank you,
Chris.
-- original message --
Hi,
SD will tau_t=0.1 will make your dynamics a lot slower.
I don't see a reason why there should be a difference between serial
and parallel.
Are all simulations single runs, or do you do restarts?
Did you compare the temperatures to check if there is no strong energy loss
or heating and if there are differences between the different simulations?
Berk
Date: Wed, 4 Feb 2009 13:35:30 -0500
From: chris.neale at utoronto.ca
To: gmx-users at gromacs.org
Subject: [gmx-users] micelle disaggregated in serial, but not
parallel, runs using sd integrator
Hello,
I have been experiencing problems with a detergent micelle falling
apart. This micelle spontaneously aggregated in tip4p and was stable
for >200 ns. I then took the .gro file from 100 ns after stable
micelle formation and began some free energy calculations, during
which the micelle partially disaggregated, even at lambda=0. At
first I thought that this was related to the free energy code, and
indeed the energygrps solution posted by Berk did stop my
to-be-annihilated detergent monomer from flying around the box even
at lambda=0.00. However, I have been able to reproduce this
disaggregation in the absence of the free-energy code, so I believe
that there is something else going on and my tests using
GMX_NO_SOLV_OPT, separate energygrps, and the code change all
indicate that this is a separate issue.
I have been trying to locate the error for a few days, but each
round of tests takes about 24h so the progress is slow. Here is a
summary of what I have learned so far.
A. Do not fall apart by 2.5 ns:
GMX 3.3.1, 4.0.2, or 4.0.3
integrator = md
energygrps = DPC SOL
tcoupl = Berendsen
tc_grps = DPC SOL
tau_t = 0.1 0.1
ref_t = 300. 300.
B. Partial dissaggregation or irregular micelle shape observed by 2.5 ns:
GMX 3.3.1, 4.0.2, or 4.0.3
integrator = sd
energygrps = System --- or --- DPC SOL
tc_grps = System
tau_t = 0.1
ref_t = 300.
* GMX 4.0.3 gives same result with "export GMX_NO_SOLV_OPT=1"
* GMX 4.0.3 gives same result when compiled with the tip4p
optimization code fix.
* GMX 4.0.3 Using tip3p in place of tip4p gives same result.
C. Does not fall apart by 7.5 ns when running section B options in parallel.
Common MDP options:
comm_mode = linear
nstcomm = 1
comm_grps = System
nstlist = 5
ns_type = grid
pbc = xyz
coulombtype = PME
rcoulomb = 0.9
fourierspacing = 0.12
pme_order = 4
vdwtype = cut-off
rvdw_switch = 0
rvdw = 1.4
rlist = 0.9
DispCorr = EnerPres
Pcoupl = Berendsen
pcoupltype = isotropic
compressibility = 4.5e-5
ref_p = 1.
tau_p = 4.0
gen_temp = 300.
gen_seed = 9896
constraints = all-bonds
constraint_algorithm= lincs
lincs-iter = 1
lincs-order = 6
gen_vel = no
unconstrained-start = yes
dt = 0.004
##################
My current hypothesis is that the sd integrator somehow functions
differently in serial than in parallel in gromacs versions 3.3.1,
4.0.2, and 4.0.3. I suspect that this is not limited to tip4p, since
I see disaggregation in tip3p also, although I did not control the
tip3p run and this may not be related to the md/sd difference.
I realize that I may have other problems, for example perhaps I
should have used dt=1.0 instead of dt=0.1 while using the sd
integrator, but the fact that a parallel run resolved the problem
makes me think that it is something else.
I am currently working to find a smaller test system, but would
appreciate it if a developer can comment on the liklihood of my
above hypothesis being correct. Also, any suggestions on sets of
mdp options that might narrow down the possibilities would be
greatly appreciated.
I have included the entire .mdp file from the 4 core job that ran
without disaggregation:
integrator = sd
comm_mode = linear
nstcomm = 1
comm_grps = System
nstlog = 50000
nstlist = 5
ns_type = grid
pbc = xyz
coulombtype = PME
rcoulomb = 0.9
fourierspacing = 0.12
pme_order = 4
vdwtype = cut-off
rvdw_switch = 0
rvdw = 1.4
rlist = 0.9
DispCorr = EnerPres
Pcoupl = Berendsen
pcoupltype = isotropic
compressibility = 4.5e-5
ref_p = 1.
tau_p = 4.0
tc_grps = System
tau_t = 0.1
ref_t = 300.
annealing = no
gen_temp = 300.
gen_seed = 9896
constraints = all-bonds
constraint_algorithm= lincs
lincs-iter = 1
lincs-order = 6
energygrps = SOL DPC DPN
; Free energy control stuff
free_energy = no
init_lambda = 0.00
delta_lambda = 0
sc_alpha = 0.0
sc-power = 1.0
sc-sigma = 0.3
couple-moltype = DPN
couple-lambda0 = vdw-q
couple-lambda1 = vdw
couple-intramol = no
nsteps = 50000
tinit = 7600
dt = 0.004
nstxout = 50000WARNING 1 [file
/scratch/4772976.1.ompi-4-21.q/md5_running/dpc50_md5.mdp, line
unknown]:
Can not couple a molecule with free_energy = no
nstvout = 50000
nstfout = 50000
nstenergy = 2500
nstxtcout = 2500
gen_vel = no
unconstrained-start = yes
####
Note that the free energy code was turned on in the above (with
lambda=0). This is because I started the debugging when I thought
that the free-energy code / tip4p combination was causing the
differences. I also ran this exact mdp file in serial and observed
disaggregation in ~2 ns.
Thank you,
Chris.
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