PRESSURE, GPRESSURE, PRESSAVG, and GPRESSAVG

From: Dennis Glass (dennisglass84_at_gmail.com)
Date: Wed Mar 18 2009 - 11:13:12 CDT

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:

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