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Note the unusually large COM velocity ...


Rick Venable
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This is a system of solvated dipeptides.

Input script:

Read .rtf & .prm
Read sequ
Generate
Read coor card .crd

Set up PBC

Minimize (Mini sd nstep 300 nprint 50)

Open .rst & .dcd

dynamics cpt leap start timestep 0.002 nstep 250000 nprint 100 iprfrq 1000 -
iunrea -1 iunwri 31 iuncrd 32 nsavv 0 nsavc 1000 nsavq -
firstt 298.0 finalt 298.0 tstruc 298.0 twindl -5.0 twindh 5.0 iseed 940829 -
ichecw 1 teminc 0.0 ihtfrq 0 ieqfrq 0 -
iasors 0 iasvel 1 iscvel 0 isvfrq 500 echeck 999999. -
inbfrq -1 imgfrq -1 ilbfrq 0 nbscale 1.5 -
cdiel eps 1.0 cutnb 15.0 cutim 15.0 ctofnb 13.0 ctonnb 9.0 vswi -
Ewald kappa 0.320 pmEwald qcor 1 order 4 fftx 64 ffty 64 fftz 64 ntrfrq 5. -
pconstant pmass 2000.0 pref 1.0 pgamma 100.0 -
Hoover tmass 1000.0 REFT 298.0

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I've tried different NTRFRQ values:

NTRFRQ=5 ----> @step#132 error: energy change tolerance exceeded
NTRFRQ=50 ---> @step#1411 error: same
NTRFRQ=100 --> @step#1518 error: same
NTRFRQ=1000 -> normal termination for 250,000 steps (500 ps)

I've run the last one for another 1 ns. It runs okay but again T is lowered every 1000 steps. I can post post parts of output if you think it's needed.

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How about posting your actual INPUT so that we have a chance of understanding what you are doing. It may also be instructive to try an NVE simulation. Are there any warning or error messages in the output?


Lennart Nilsson
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Okay here is the actual input (I'll put the generation of 50 peptides in a loop eventually..):

* 50 nonpolarizable peptides and 1000 nonpolarizable waters
* Equilibration (NPT) 1 ns
*

PRNLV 5 NODE 0
WRNLV 5 NODE 0

!! Set the threshold for error reporting.
bomb -1

! Read structure and parameter files
read rtf card name ~/charmm-c34b2-mod-gnu-mpi-xxl/toppar/top_all22_prot.inp
read param card name ~/charmm-c34b2-mod-gnu-mpi-xxl/toppar/par_all22_prot.inp

read sequ card
2
ALA PRO
generate x1 first nter last cter setup
read sequ card
2
ALA PRO
generate x2 first nter last cter setup
read sequ card
2
ALA PRO
generate x3 first nter last cter setup

............ DO READ SEQU & GENE 50 TIMES

read sequ card
2
ALA PRO
generate x50 first nter last cter setup
read sequ TIP3 1000
gene TIP3 first none last none noang nodihed
read coor card appe name ./ntr/1000-1.crd

coor stats

!============== SET UP PBC ========================

crystal defined cubi 36.5 36.5 36.5 90.0 90.0 90.0

crystal build cutoff 15 noper 0

imag byres xcen 0 ycen 0 zcen 0 select segid TIP3 end
imag byseg xcen 0 ycen 0 zcen 0 select .not. segid TIP3 end

FASTER ON
SHAKE BONH PARAM SELE segid TIP3 END

!========== MINIMIZE ================================

mini sd nstep 300 nprint 50

open unit 1 write form name ./ntr/trial-mini.pdb
write coor pdb unit 1
*

!===================== DYNAMICS ==== ====================

open write unit 31 card name ./ntr/1000-1.rst
open write unit 32 unformatted name ./ntr/1000-1.dcd

dynamics cpt leap start timestep 0.002 nstep 500000 nprint 100 iprfrq 1000 -
iunrea -1 iunwri 31 iuncrd 32 nsavv 0 nsavc 1000 -
firstt 298.0 finalt 298.0 tstruc 298.0 twindl -5.0 twindh 5.0 -
ichecw 1 teminc 0.0 ihtfrq 0 ieqfrq 0 -
iasors 0 iasvel 1 iscvel 0 isvfrq 500 echeck 999999. -
inbfrq -1 imgfrq -1 ilbfrq 0 nbscale 1.5 -
cdiel eps 1.0 cutnb 15.0 cutim 15.0 ctofnb 13.0 ctonnb 9.0 vswi -
Ewald kappa 0.320 pmEwald qcor 1 order 4 fftx 64 ffty 64 fftz 64 ntrfrq 1000. -
pconstant pmass 2000.0 pref 1.0 pgamma 100.0 -
Hoover tmass 1000.0 REFT 298.0

open write unit 24 card name ./ntr/1000-1.crd
write coordinates sele all end card unit 24
*

open unit 1 write form name ./ntr/1000-1.pdb
write coor pdb unit 1
*

stop

No warnings or error messages in the output.

Last edited by TGK; 10/28/09 03:58 PM.
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A 2 fs timestep is not recommended for CPT dynamics.

Do not use such a large ECHECK value, it only masks model building problems you should deal with.

The use of the legacy ISVFRQ feature is no longer recommended.

Possibly harmless, but ICHECW should be zero with a thermostat; however, you should consider heating from e.g. 198 K.

ORDER 6 is recommended with PME.

TMASS is in different units than PMASS, and is typically 5-10 times larger than PMASS.


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I've tried NVE (restarted from 500 ps NPT simulation) and here is the dynamics script with everything else being same as above:

dynamics cpt leap restart timestep 0.002 nstep 500000 nprint 100 iprfrq 1000 -
iunrea 30 iunwri 31 iuncrd 32 nsavv 0 nsavc 1000 -
firstt 298.0 finalt 298.0 tstruc 298.0 twindl -5.0 twindh 5.0 -
ichecw 1 teminc 0.0 ihtfrq 0 ieqfrq 0 -
iasors 0 iasvel 1 iscvel 0 isvfrq 500 echeck 999999. -
inbfrq -1 imgfrq -1 ilbfrq 0 nbscale 1.5 -
cdiel eps 1.0 cutnb 15.0 cutim 15.0 ctofnb 13.0 ctonnb 9.0 vswi -
Ewald kappa 0.320 pmEwald qcor 1 order 4 fftx 64 ffty 64 fftz 64 ntrfrq 1000. -
pconstant pmass 0.0 pref 1.0 pgamma 100.0

Below is the energy/T values:

DYNA> 0 500.00000 -11527.40089 2231.61253 -13759.01342 223.54902
DYNA> 100 500.20000 -7590.82452 4424.69999 -12015.52451 443.23884
DYNA> 200 500.40000 -7611.27369 4441.45383 -12052.72752 444.91714
DYNA> 300 500.60000 -7591.22003 4410.11250 -12001.33253 441.77756
DYNA> 400 500.80000 -7613.04009 4416.59719 -12029.63728 442.42715
DYNA> 500 501.00000 -7615.28653 4452.09875 -12067.38529 445.98348
DYNA> 600 501.20000 -7602.65421 4443.41112 -12046.06533 445.11321
DYNA> 700 501.40000 -7591.89844 4403.24306 -11995.14150 441.08942
DYNA> 800 501.60000 -7589.63852 4372.28588 -11961.92440 437.98832
DYNA> 900 501.80000 -7591.36921 4393.83868 -11985.20789 440.14735
DYNA> 1000 502.00000 -7591.93781 4410.91451 -12002.85232 441.85790
DYNA> 1000 502.00000 -10004.66639 1998.18593 -12002.85232 200.16580
DYNA> 1100 502.20000 -8038.45814 4256.58078 -12295.03892 426.39771
DYNA> 1200 502.40000 -8038.36114 4244.92171 -12283.28285 425.22977
DYNA> 1300 502.60000 -8047.50012 4234.38436 -12281.88448 424.17421
DYNA> 1400 502.80000 -8052.87790 4314.06582 -12366.94371 432.15620
DYNA> 1500 503.00000 -8053.39363 4227.22242 -12280.61605 423.45677
DYNA> 1600 503.20000 -8033.52436 4114.02614 -12147.55050 412.11747
DYNA> 1700 503.40000 -8041.05603 4274.55719 -12315.61322 428.19847
DYNA> 1800 503.60000 -8051.31112 4236.61516 -12287.92629 424.39768
DYNA> 1900 503.80000 -8049.60861 4290.50733 -12340.11594 429.79626
DYNA> 2000 504.00000 -8040.69284 4230.58699 -12271.27984 423.79381
DYNA> 2000 504.00000 -10648.38228 1622.89756 -12271.27984 162.57175
DYNA> 2100 504.20000 -9815.45014 3301.59056 -13117.04070 330.73275

.....................................................

DYNA> 92400 684.80000 -9675.97579 3590.35193 -13266.32772 359.65906
DYNA> 92500 685.00000 -9682.29828 3646.00700 -13328.30527 365.23424
DYNA> 92600 685.20000 -9672.07731 3595.31018 -13267.38749 360.15575
DYNA> 92700 685.40000 -9673.77183 3650.65161 -13324.42344 365.69950
DYNA> 92800 685.60000 -9670.74213 3600.13626 -13270.87839 360.63919
DYNA> 92900 685.80000 -9672.35338 3604.10724 -13276.46062 361.03698
DYNA> 93000 686.00000 -9672.20563 3624.48801 -13296.69365 363.07860
DYNA> 93000 686.00000 -11512.49864 1784.19500 -13296.69365 178.72952
DYNA> 93100 686.20000 -9376.05405 3676.77147 -13052.82551 368.31603
DYNA> 93200 686.40000 -9375.38001 3634.22421 -13009.60422 364.05391
DYNA> 93300 686.60000 -9374.84352 3766.53687 -13141.38038 377.30817
DYNA> 93400 686.80000 -9376.96369 3702.26466 -13079.22835 370.86978
DYNA> 93500 687.00000 -9376.66604 3741.87003 -13118.53607 374.83720
DYNA> 93600 687.20000 -9373.05923 3688.15849 -13061.21772 369.45671
DYNA> 93700 687.40000 -9386.97523 3769.58427 -13156.55950 377.61344
DYNA> 93800 687.60000 -9369.67804 3688.06368 -13057.74172 369.44721
DYNA> 93900 687.80000 -9371.54561 3726.86297 -13098.40858 373.33388
DYNA> 94000 688.00000 -9381.83079 3729.27931 -13111.11010 373.57594
DYNA> 94000 688.00000 -10983.01524 2128.09487 -13111.11010 213.17927
DYNA> 94100 688.20000 -7748.95337 4480.06713 -12229.02050 448.78518

......................................................

DYNA> 121000 742.00000 -13101.20459 2183.13101 -15284.33560 218.69245
DYNA> 121000 742.00000 -14155.19472 1129.14088 -15284.33560 113.11029
DYNA> 121100 742.20000 -12761.91199 2360.86605 -15122.77803 236.49683
DYNA> 121200 742.40000 -12747.98203 2358.97959 -15106.96162 236.30786
DYNA> 121300 742.60000 -12735.09192 2379.51800 -15114.60992 238.36527
DYNA> 121400 742.80000 -12743.79433 2365.37450 -15109.16882 236.94846
DYNA> 121500 743.00000 -12755.90569 2369.47706 -15125.38275 237.35943
DYNA> 121600 743.20000 -12769.17609 2430.55795 -15199.73404 243.47813
DYNA> 121700 743.40000 -12773.69441 2404.36060 -15178.05502 240.85385
DYNA> 121800 743.60000 -12760.88229 2409.46181 -15170.34410 241.36485
DYNA> 121900 743.80000 -12750.56206 2395.91414 -15146.47619 240.00773
DYNA> 122000 744.00000 -12736.72028 2376.45971 -15113.18000 238.05891
DYNA> 122000 744.00000 -13722.62372 1390.55628 -15113.18000 139.29725
DYNA> 122100 744.20000 -11599.53305 2900.51418 -14500.04723 290.55542
DYNA> 122200 744.40000 -11580.92838 2854.85623 -14435.78460 285.98169
DYNA> 122300 744.60000 -11590.09074 2921.69144 -14511.78218 292.67682
DYNA> 122400 744.80000 -11586.87481 2850.74130 -14437.61611 285.56948
DYNA> 122500 745.00000 -11593.79837 2932.09261 -14525.89098 293.71875
DYNA> 122600 745.20000 -11605.81224 2925.98623 -14531.79847 293.10705
DYNA> 122700 745.40000 -11593.00068 2868.53171 -14461.53239 287.35161
DYNA> 122800 745.60000 -11600.53552 2929.50784 -14530.04335 293.45982
DYNA> 122900 745.80000 -11585.96591 2900.31683 -14486.28274 290.53565

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I believe that reduces to NVE with PMASS 0., but that is not the usual way to do NVE dynamics. Since the T appears to be dropping, it is unlikely that system has been equilibrated sufficiently for NVE dynamics. The other dynamics options remain sub-optimal.


Rick Venable
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I've run two scripts: modified equilibration and heating

Here is the equilibration script and DYNA> results so far:

dynamics cpt leap restart timestep 0.001 nstep 250000 nprint 100 iprfrq 1000 -
iunrea 30 iunwri 31 iuncrd 32 nsavv 0 nsavc 1000 -
firstt 298.0 finalt 298.0 tstruc 298.0 twindl -5.0 twindh 5.0 -
ichecw 0 teminc 0.0 ihtfrq 0 ieqfrq 0 -
iasors 0 iasvel 1 iscvel 0 -
inbfrq -1 imgfrq -1 ilbfrq 0 nbscale 1.5 -
cdiel eps 1.0 cutnb 15.0 cutim 15.0 ctofnb 13.0 ctonnb 9.0 vswi -
Ewald kappa 0.320 pmEwald qcor 1 order 6 fftx 48 ffty 48 fftz 48 ntrfrq 1000. -
pconstant pmass 2000.0 pref 1.0 pgamma 100.0 -
Hoover tmass 20000.0 REFT 298.0

DYNA> 75000 325.00000 -10140.97658 3057.04807 -13198.02465 306.23600
DYNA> 75000 325.00000 -11896.35710 1301.66755 -13198.02465 130.39293
DYNA> 75100 325.10000 -11052.03320 2789.77185 -13841.80505 279.46194
DYNA> 75200 325.20000 -10679.61940 2964.16917 -13643.78857 296.93198
DYNA> 75300 325.30000 -10205.48991 3118.69718 -13324.18710 312.41163
DYNA> 75400 325.40000 -10100.53697 3147.35707 -13247.89404 315.28260
DYNA> 75500 325.50000 -10335.98988 2960.80954 -13296.79942 296.59543
DYNA> 75600 325.60000 -10507.17755 2821.63700 -13328.81455 282.65399
DYNA> 75700 325.70000 -10475.86189 2880.62873 -13356.49062 288.56342
DYNA> 75800 325.80000 -10288.05895 2969.86504 -13257.92399 297.50255
DYNA> 75900 325.90000 -10158.80487 3162.96183 -13321.76670 316.84578
DYNA> 76000 326.00000 -10312.31747 2986.21211 -13298.52957 299.14010
DYNA> 76000 326.00000 -12298.78181 999.74776 -13298.52957 100.14849
DYNA> 76100 326.10000 -11406.94257 2828.99874 -14235.94132 283.39145
DYNA> 76200 326.20000 -10170.87361 3524.04683 -13694.92044 353.01703
DYNA> 76300 326.30000 -10203.10057 3307.37302 -13510.47359 331.31200
DYNA> 76400 326.40000 -11144.88978 2803.54803 -13948.43781 280.84195
DYNA> 76500 326.50000 -11636.61754 2575.83188 -14212.44941 258.03077
DYNA> 76600 326.60000 -11293.25438 2853.61606 -14146.87043 285.85745
DYNA> 76700 326.70000 -10571.15873 3265.49547 -13836.65420 327.11696
DYNA> 76800 326.80000 -10469.49251 3248.98864 -13718.48114 325.46341
DYNA> 76900 326.90000 -10994.11222 2924.32620 -13918.43842 292.94076
DYNA> 77000 327.00000 -11385.75582 2728.35178 -14114.10761 273.30926
DYNA> 77000 327.00000 -13088.16626 1025.94134 -14114.10761 102.77240
DYNA> 77100 327.10000 -11789.64512 2590.77319 -14380.41831 259.52750
DYNA> 77200 327.20000 -10376.58335 3414.66164 -13791.24499 342.05950
DYNA> 77300 327.30000 -9745.87942 3495.56018 -13241.43960 350.16341
DYNA> 77400 327.40000 -10478.13497 2960.43052 -13438.56550 296.55746
DYNA> 77500 327.50000 -11143.13492 2610.39583 -13753.53074 261.49317
DYNA> 77600 327.60000 -11091.70639 2712.78855 -13804.49494 271.75023
DYNA> 77700 327.70000 -10508.26224 3139.45024 -13647.71248 314.49054
DYNA> 77800 327.80000 -10159.07518 3168.53495 -13327.61012 317.40406
DYNA> 77900 327.90000 -10333.66821 3049.28462 -13382.95282 305.45831
DYNA> 78000 328.00000 -10729.01813 2874.14846 -13603.16659 287.91426
DYNA> 78000 328.00000 -12503.74710 1099.41949 -13603.16659 110.13299
DYNA> 78100 328.10000 -11501.25517 2549.82973 -14051.08490 255.42604
DYNA> 78200 328.20000 -10224.27337 3268.01409 -13492.28747 327.36926
DYNA> 78300 328.30000 -9369.20666 3462.90089 -12832.10755 346.89181
DYNA> 78400 328.40000 -9831.02251 3164.72480 -12995.74731 317.02239
DYNA> 78500 328.50000 -10604.89678 2732.38226 -13337.27904 273.71301
DYNA> 78600 328.60000 -10789.16722 2745.69765 -13534.86486 275.04686
DYNA> 78700 328.70000 -10393.72737 2921.09456 -13314.82193 292.61703
DYNA> 78800 328.80000 -9852.63053 3194.14708 -13046.77761 319.96973
DYNA> 78900 328.90000 -9785.59355 3144.70924 -12930.30279 315.01735
DYNA> 79000 329.00000 -10170.46232 2946.89310 -13117.35542 295.20137
DYNA> 79000 329.00000 -11831.68648 1285.66894 -13117.35542 128.79029
DYNA> 79100 329.10000 -10987.29610 2700.58337 -13687.87947 270.52759
DYNA> 79200 329.20000 -10504.78060 2925.73220 -13430.51280 293.08160
DYNA> 79300 329.30000 -9837.05187 3226.49429 -13063.54616 323.21007
DYNA> 79400 329.40000 -9803.13977 3197.28922 -13000.42898 320.28449
DYNA> 79500 329.50000 -10291.16794 2894.69331 -13185.86125 289.97232
DYNA> 79600 329.60000 -10593.51645 2800.36140 -13393.87785 280.52274
DYNA> 79700 329.70000 -10498.73383 2898.28594 -13397.01976 290.33220
DYNA> 79800 329.80000 -10182.06678 3042.90473 -13224.97151 304.81921
DYNA> 79900 329.90000 -9982.94186 3078.69916 -13061.64103 308.40488
DYNA> 80000 330.00000 -10111.16869 3014.02765 -13125.19634 301.92649
DYNA> 80000 330.00000 -12009.48703 1115.70931 -13125.19634 111.76480
DYNA> 80100 330.10000 -11125.79330 2699.94217 -13825.73547 270.46336

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Rick Venable
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