Re: PRESSURE, GPRESSURE, PRESSAVG, and GPRESSAVG

From: Sebastian Stolzenberg (s.stolzenberg_at_gmail.com)
Date: Wed Nov 04 2009 - 18:10:32 CST

Dear All,

My system is showing the same output behavior (reasonable values for all
four observables except for PRESSURE), though I am not using molly.

I am using a script (attached) from a Prof. in our lab, a script, which
works fine for his system (PRESSURE values fluctuate around 1 bar).

However, my system (250K atoms) is much larger than his (80K atoms). Is
that the possible reason for the difference in PRESSURE output?

I am using both NAMD 2.6 and 2.7

Thank you,
Sebastian

Have you tried without MOLLY? It is a seldom-used option and I know it
has caused pressure problems in the past. You'll want to reduce your
fullelectfreq to compensate for turning it off...

As far as the actual pressure of your system, you need to take a long
timescale average of one of the pressure fields (PRESSAVG or GPRESSAVG
are good choices) *after* your system has equilibrated, which yours
certainly has not until near the end of your run, and possibly not even
then.

Best,
Peter

Dennis Glass wrote:
> Hello,
>
> I am confused by the outputted PRESSURE, GPRESSURE, PRESSAVG, and
> GPRESSAVG values.
> - What is the actual pressure of my system?
> - Is there an issue with my MD because PRESSURE is far away from
GPRESSURE,
> PRESSAVG, and GPRESSAVG values?
>
> According to the user guide, it is:"PRESSURE is the pressure calculated
> based on individual atoms, while GPRESSURE incorporates hydrogen
atoms into
> the heavier atoms to which they are bonded, producing smaller
fluctuations.
> The TEMPAVG, PRESSAVG, and GPRESSAVG are the average of temperature and
> pressure values since the previous ENERGY output"
> To my understanding, PRESSURE, GPRESSURE, PRESSAVG, and GPRESSAVG should
> fluctuate around the same mean value.
>
> However, for my NPT simulation (using langevin barostat set to 1 bar),
> PRESSURE is far away from GPRESSURE, PRESSAVG, and GPRESSAVG. PRESSURE
> fluctuates around -19500, whereas GPRESSURE, PRESSAVG, and GPRESSAVG
> fluctuate around 0. This simulation used rigidbonds for TIP3P water only
> with the settle algorithm.
> In a second simulation with equal parameters but without rigidbonds
> (rigidbonds none), PRESSURE fluctuates around -2500, whereas GPRESSURE,
> PRESSAVG, and GPRESSAVG again fluctuates around 0.
>
> Thanks for your help
> Dennis
>
>
>
> Below, you will find:
> - My configuration file
> - Sample output for both runs
>
> Here is my configuration file. The only difference between my two runs is
> the parameter rigidbonds which is "water" or "none"
>
>
###########################################################################
> ##### periodic boundary conditions
>
###########################################################################
>
> cellBasisVector1 75.0 0.0 0.0
> cellBasisVector2 0.0 75.0 0.0
> cellBasisVector3 0.0 0.0 75.0
> cellOrigin 37.6563415527 37.3194503784 37.4159545898
> xstfile equil001.xst
> xstfreq 600 # same as dcd freq
> wrapwater on # off is default
> wrapall off # off is default
>
> #####################################################################
> ##### simulation space partitioning
> #####################################################################
> cutoff 12.0 # both estat and vdw
> switching on
> switchdist 10.0
> pairlistdist 14.0
>
> #####################################################################
> ##### timestep parameters
> #####################################################################
> numsteps 1000000
> timestep 1.0
> firsttimestep 0
> stepspercycle 24
>
> #####################################################################
> ##### basic dynamics
> #####################################################################
> exclude scaled1-4
> 1-4scaling 1.0
> temperature 310.0 # initial temperature (K)
> dielectric 1.0 # default
> rigidbonds water # options : none,water,all
> rigidtolerance 1.0e-8
> rigiditerations 100
> usesettle on #faster than SHAKE , only for water
>
> #####################################################################
> ##### PME parameters
> #####################################################################
> pme yes # 'on' is also possible
> pmegridsizex 75
> pmegridsizey 75
> pmegridsizez 75
> pmeinterporder 6
>
> #####################################################################
> ##### Multiple timestep parameters
> #####################################################################
> fullelectfrequency 6
> nonbondedfreq 2
> mtsalgorithm impulse
> longsplitting c1
> molly on
> mollytolerance 0.00001 #default
> mollyiterations 100 #default
>
> #####################################################################
> # Temperature control
> #####################################################################
> # Langevib dynamics parameters
> #####################################################################
>
> langevin on
> langevintemp 310.0
> langevindamping 5.0
>
> langevinpiston on # NVT(off), NPT(on)
> langevinpistontarget 1.0
> langevinpistonperiod 200.0
> langevinpistondecay 100.0
> langevinpistontemp 310.0
>
> #####################################################################
> ##### I/O
> #####################################################################
>
> # input files
> coordinates mini002_out.coor
> structure 2pc0-w-box-ionized.psf # Xplore PSF file
> parameters par_all27_prot_na.inp # parameter file (CHARMM)
> paratypecharmm on # (on or off) or (yes or no)
>
> # output files
> outputname equil001_out
> binaryoutput no
> restartname equil001_rst
> restartfreq 600
> binaryrestart yes # default
> dcdfile equil001_traj.dcd
> dcdfreq 600
> dcdunitcell yes
> veldcdfile equil001_traj.vel
> veldcdfreq 600
>
> # standard output
> outputenergies 600
> outputmomenta 600
> outputpressure 600
> outputtiming 600
>
>
>
>
>
>
>
>
> And here is what I "grepped" from the output for CASE 1 and two. A
complete
> extract of the output is further below.
> CASE 1 - rigidbonds water
>
> ETITLE: TS BOND ANGLE DIHED
> IMPRP ELECT VDW BOUNDARY
> MISC KINETIC TOTAL TEMP
> TOTAL2 TOTAL3 TEMPAVG PRESSURE
> GPRESSURE VOLUME PRESSAVG GPRESSAVG
> ENERGY: 0 156.2295 477.6366 543.1516
> 14.1392 -186016.4768 22326.3771 0.0000 0.0000
> 26692.0530 -135806.8898 311.5979 -135804.0197
> -135804.0197 311.5979 -26619.9688 -993.8260
> 421875.0000 -26619.9688 -993.8260
> ENERGY: 600 1099.1669 1696.8265 785.3375
> 107.7177 -149752.5773 14214.5129 0.0000
> 0.0000 25301.2494 -106547.7664 295.3620 -106492.3115
> -106501.1760 254.2189 -20122.1543 -105.7462
> 420264.4922 4.8423 -6.2990
> ENERGY: 1200 1111.0196 1759.9218 792.2553
> 107.3503 -145138.4867 12938.2441 0.0000
> 0.0000 26161.6491 -102268.0465 305.4061 -102211.1077
> -102212.3342 303.0467 -19393.8014 110.3821
> 417513.9446 9.5976 8.2886
> ENERGY: 1800 1098.8792 1792.1959 782.4552
> 100.9114 -143734.8057 12291.5641 0.0000
> 0.0000 26531.1722 -101137.6278 309.7198 -101081.4981
> -101077.3634 308.5917 -19189.2141 168.9799
> 413247.6025 -11.3537 -12.7753
> ENERGY: 2400 1142.2458 1804.9680 810.0859
> 105.7437 -143174.5213 11953.1843 0.0000
> 0.0000 26511.9608 -100846.3328 309.4956 -100787.1216
> -100789.6523 310.4971 -19408.4126 -43.8252
> 413249.3866 -11.5525 -13.6493
> ENERGY: 3000 1066.4982 1750.9340 810.7888
> 104.0372 -143144.7402 11753.0165 0.0000
> 0.0000 26732.6482 -100926.8173 312.0718 -100871.1054
> -100867.3411 310.3368 -19377.3162 -103.7912
> 411992.3521 -21.2331 -21.4404
> ENERGY: 3600 1117.5124 1844.6898 782.5543
> 103.8984 -143726.3790 12066.7927 0.0000
> 0.0000 26608.8667 -101202.0648 310.6268 -101140.6386
> -101156.4608 309.5742 -19373.3331 -21.6161
> 411517.2798 -4.3175 -2.9677
> ENERGY: 4200 1152.4483 1819.3689 795.1798
> 103.7243 -143024.6388 11730.7400 0.0000
> 0.0000 26534.8606 -100888.3168 309.7629 -100830.3879
> -100831.4452 309.7743 -19461.8980 -139.7088
> 411906.6004 10.9361 8.4910
> ENERGY: 4800 1164.9692 1755.3011 797.4557
> 117.9048 -142939.3028 11708.6195 0.0000
> 0.0000 26610.0723 -100784.9802 310.6409 -100724.5157
> -100732.6681 310.7123 -19492.3951 -126.1225
> 412233.8710 -11.2586 -9.1837
> ENERGY: 5400 1132.1406 1784.3478 791.7675
> 102.0435 -143210.6328 12040.7669 0.0000
> 0.0000 26599.5741 -100759.9923 310.5184 -100702.1455
> -100700.3935 310.8472 -19094.1634 216.0380
> 412114.1689 1.9672 3.8559
> ENERGY: 6000 1096.7557 1718.0942 787.4531
> 103.8353 -143263.0316 11831.1583 0.0000
> 0.0000 26647.9832 -101077.7519 311.0835 -101020.6649
> -101018.4213 310.8902 -19447.2452 -16.5729
> 411006.1955 7.6893 9.5044
> ENERGY: 6600 1125.6144 1770.0440 779.9699
> 107.3056 -143319.5800 11925.5402 0.0000
> 0.0000 26669.9584 -100941.1475 311.3400 -100878.5597
> -100896.9775 309.7383 -19192.3687 34.7166
> 410406.1816 -5.6569 -4.5457
> ENERGY: 7200 1060.4996 1794.4555 752.2321
> 105.3001 -143180.1432 11894.8730 0.0000
> 0.0000 26532.8380 -101039.9449 309.7393 -100981.6702
> -100983.6941 309.7362 -19287.2294 -62.5663
> 411840.7574 -12.4793 -11.0744
> ENERGY: 7800 1083.2277 1808.3939 791.8922
> 92.3827 -143272.5783 12023.4117 0.0000 0.0000
> 26470.3013 -101002.9687 309.0092 -100941.5147
> -100955.4854 310.4582 -19246.6608 129.2379
> 411382.3753 -2.3195 -2.3465
> ENERGY: 8400 1068.2619 1765.8127 819.5024
> 96.6999 -143224.9192 11995.6586 0.0000 0.0000
> 26665.5385 -100813.4452 311.2884 -100761.6883
> -100739.4323 310.5851 -19266.1105 119.2516
> 411260.3205 3.3641 3.0068
> ENERGY: 9000 1069.2441 1737.3903 815.1489
> 86.1444 -142853.8095 11754.7603 0.0000 0.0000
> 26595.7280 -100795.3934 310.4735 -100740.1788
> -100731.2056 311.9157 -19433.3870 -62.0919
> 412067.7287 1.5083 1.6525
> ENERGY: 9600 1099.4435 1788.6563 787.0911
> 93.1993 -143220.8657 11688.8761 0.0000 0.0000
> 26583.7986 -101179.8008 310.3342 -101116.5815
> -101136.5161 310.3395 -19347.0110 -68.3492
> 410172.0744 -3.4694 -1.7593
>
> CASE 2 - rigidbonds none
>
> ETITLE: TS BOND ANGLE DIHED
> IMPRP ELECT VDW BOUNDARY
> MISC KINETIC TOTAL TEMP
> TOTAL2 TOTAL3 TEMPAVG PRESSURE
> GPRESSURE VOLUME PRESSAVG GPRESSAVG
> ENERGY: 0 6321.3326 4159.5593 543.1516
> 14.1392 -205927.2625 22777.1974 0.0000 0.0000
> 38303.8846 -133807.9979 309.4063 -133565.7858
> -133565.7858 309.4063 -1265.1690 -4055.4148
> 421875.0000 -1265.1690 -4055.4148
> ENERGY: 600 13243.3583 8782.8045 787.3107
> 96.9621 -170350.3114 18523.2823 0.0000 0.0000
> 36564.6522 -92351.9413 295.3573 -91775.4971
> -91811.0444 257.0516 3300.6198 215.3346
> 410979.9631 -6.2811 -9.8963
> ENERGY: 1200 13490.2624 8843.2353 837.7827
> 100.8493 -165765.4741 16701.1279 0.0000
> 0.0000 37975.5709 -87816.6456 306.7543 -87246.2701
> -87227.0852 303.5954 2171.2760 -117.4800
> 409270.2039 10.1164 9.7044
> ENERGY: 1800 13416.4833 8880.2737 820.1875
> 101.9738 -164278.3947 16116.2708 0.0000
> 0.0000 37992.1718 -86951.0337 306.8884 -86379.1905
> -86367.5571 308.9495 2283.3581 -126.9908
> 405551.7017 -9.6859 -9.4708
> ENERGY: 2400 13386.1140 8859.1454 771.4590
> 103.4271 -163962.6322 15960.6661 0.0000
> 0.0000 38429.4925 -86452.3280 310.4209 -85880.4596
> -85875.9606 309.4829 2540.4132 -1.2795
> 403251.4013 31.4472 30.7272
> ENERGY: 3000 13428.2949 9159.6635 798.7912
> 103.7521 -163545.6394 15639.9981 0.0000
> 0.0000 38516.0688 -85899.0707 311.1202 -85332.6354
> -85313.0578 309.7732 2560.1071 -115.9919
> 402456.2861 19.4607 19.2724
> ENERGY: 3600 13157.2745 8824.3536 786.0347
> 96.1197 -163524.6154 15718.2584 0.0000 0.0000
> 38296.1031 -86646.4713 309.3434 -86076.9976
> -86076.9567 310.0757 3411.5336 47.1838
> 401729.3303 12.9019 14.0255
> ENERGY: 4200 13300.0279 9003.7319 802.8325
> 99.1417 -164162.3897 16063.5830 0.0000 0.0000
> 38266.9032 -86626.1695 309.1075 -86050.7724
> -86072.0392 309.9457 2973.5014 482.0076
> 400307.0041 17.5071 19.1756
> ENERGY: 4800 13463.2529 9094.2650 803.1044
> 99.2776 -163857.5458 15662.0253 0.0000 0.0000
> 38310.0118 -86425.6089 309.4558 -85864.5342
> -85826.7855 310.3919 2051.7287 -120.8509
> 403225.5164 27.8780 28.3869
> ENERGY: 5400 13591.6862 8964.1299 788.9305
> 117.7095 -164434.6896 16103.9891 0.0000
> 0.0000 38487.0423 -86381.2021 310.8858 -85808.5333
> -85799.8281 310.7104 2325.9510 100.3194
> 402296.0275 3.4884 1.1373
> ENERGY: 6000 13319.4823 8978.3929 777.1531
> 91.9300 -164146.4685 15836.4725 0.0000 0.0000
> 38725.0199 -86418.0178 312.8081 -85846.3113
> -85836.6895 310.4400 2649.0353 126.3629
> 402059.5961 27.9801 26.3815
> ENERGY: 6600 13507.5174 9075.2055 818.1999
> 102.6575 -164285.3944 15890.1085 0.0000
> 0.0000 38749.3581 -86142.3475 313.0047 -85577.1895
> -85541.6149 310.6259 2337.0176 48.8901
> 401707.0401 10.3194 12.9774
> ENERGY: 7200 13419.5342 9001.9223 798.3572
> 83.9034 -163906.1739 15661.4110 0.0000 0.0000
> 38449.8590 -86491.1869 310.5854 -85923.4447
> -85905.5683 310.6418 2150.1098 -222.8914
> 402539.5744 16.5795 15.4230
> ENERGY: 7800 13381.2232 8894.6914 773.1108
> 99.9992 -163869.0803 15673.5924 0.0000 0.0000
> 38426.5986 -86619.8647 310.3975 -86049.2804
> -86040.5464 310.1115 2982.2628 -27.4440
> 401801.6911 7.8299 8.6826
> ENERGY: 8400 13446.1373 9143.0554 776.5691
> 100.2917 -164396.8540 16112.7228 0.0000
> 0.0000 38473.3820 -86344.6957 310.7754 -85766.7615
> -85785.5246 310.2638 2864.4527 264.1857
> 400305.8017 42.8993 42.4011
> ENERGY: 9000 13525.3991 8939.4828 768.4597
> 101.8802 -163706.3025 15759.3027 0.0000
> 0.0000 38358.7638 -86253.0142 309.8496 -85672.6607
> -85694.5384 310.9604 2527.1748 -0.1126
> 401587.5878 -2.0186 -0.6449
> ENERGY: 9600 13380.9943 8992.1108 787.1335
> 97.1782 -164299.3628 15905.8130 0.0000 0.0000
> 38163.9772 -86972.1558 308.2761 -86407.3406
> -86373.0628 310.2888 2514.8453 129.9850
> 400610.2521 8.9998 10.0426
>
>
>
> Complete output:
>

set indir input
set outdir output

set temperature 310
set restartname $mysystem\_equil_phase8u.restart
set outputname $mysystem\_equil_phase8v

structure $indir/$mysystem\_ionized_cmap.psf
coordinates $indir/$mysystem\_ionized_cmap.pdb
bincoordinates $outdir/$restartname.coor
binvelocities $outdir/$restartname.vel
extendedSystem $outdir/$restartname.xsc
firsttimestep 0

# Input
paraTypeCharmm on
parameters $common/toppar/par_all27_prot_lipid.prm

# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 12.
switching on
switchdist 10.
pairlistdist 13.5
margin 1.5

# Integrator Parameters
timestep 1.0 ;# 1fs/step
rigidBonds all ;# needed for 2fs steps
rigidTolerance 0.00000001
nonbondedFreq 2
fullElectFrequency 4
stepspercycle 20

# Constant Temperature Control
langevin on ;# do langevin dynamics
langevinDamping 1 ;# damping coefficient (gamma)
langevinTemp $temperature
langevinHydrogen off ;# don't couple langevin bath to hydrogens

LangevinPiston on
LangevinPistonTarget 1.01325
LangevinPistonPeriod 200
LangevinPistonDecay 50
LangevinPistonTemp $temperature

wrapAll on

# PME (for full-system periodic electrostatics)
PME yes
PMEGridSpacing 1.0

# Constant Pressure Control (variable volume)
useGroupPressure yes ;# needed for rigidBonds
useFlexibleCell yes
useConstantArea no

# Output
outputName $outdir/$outputname

restartfreq 5000 ;# 500steps = every 0.5ps
dcdfreq 5000
xstFreq 5000
outputEnergies 5000
outputPressure 5000

binaryoutput yes
binaryrestart yes
outputTiming 5000

set totalrunsteps 10000
run $totalrunsteps

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