Subject: help about NAMD

From: wei <[email-masked]>
Date: Thu, 5 Dec 2002 12:03:37 -0500

Dear all:

I want to use langevin piston method for pressure control in NAMD, my system is pretty big (about 40000 atoms), 
and following is part of my config file:

*****************************************
#NPT ENSEMBLE
#Langevin dynamics
langevin  on    # do langevin dynamics
langevinDamping 5  # damping coefficient (gamma) of 5/ps
langevinTemp  300 # bath temperature
langevinHydrogen  no  # don't couple langevin bath to hydrogens

# pressure
langevinPiston          on
langevinPistonTarget    1.01325 #  in bar -> 1 atm
langevinPistonPeriod    200
langevinPistonDecay     500
langevinPistonTemp      300
useGroupPressure        yes
***********************************************

however, in the output (following is part of it), the pressure seems to be oscillating and far from the value I want:

******************************************
PRESSURE:   1830 39.2187 61.488 84.0019 61.488 22.6415 -37.0633 84.0019 -37.0633 28.6089
GPRESSURE: 1830 111.13  24.1343 100.18 151.549 81.3152 -31.7188 52.9986 -64.2686 96.83
ENERGY:      1830 1389.1377   3961.1676   2096.5308   290.2453    -309817.7510 26803.1094  0.0000      0.0000      52417.3218  -222860.2384 297.0
166    30.1564(this is the PRESSURE)     96.4250(THIS IS THE GPRESSURE)     859153.1859 -6.8394     5.7249
PRESSURE: 1840 -44.1607 47.0822 87.6176 47.0822 -76.5632 24.8784 87.6176 24.8784 -194.227
GPRESSURE: 1840 -1.39699 73.4161 86.3096 -29.9097 5.18774 -1.7759 55.9111 70.4077 -115.03
ENERGY:   1840 1366.7693   3995.7682   2121.9492   287.2088    -309756.6577 26597.6246  0.0000      0.0000      52664.2251  -222723.1125 298.4
156    -104.9835(PRESSURE)   -37.0798(GPRESSURE)    859352.4078 -38.0042    -26.2113
PRESSURE: 1850 -48.9295 -121.345 -97.5314 -121.345 -5.10953 1.36691 -97.5314 1.36691 -53.157
GPRESSURE: 1850 26.8483 -81.3571 -168 -136.568 60.8743 23.3167 -11.4935 3.17469 2.01779
ENERGY:   1850 1352.3590   3971.5419   2109.2767   275.2429    -309848.9843 26611.7573  0.0000      0.0000      52870.0527  -222658.7538 299.5
819    -35.7320(PRESSURE)    29.9135(GPRESSURE)     859526.6482 77.2794     86.5364
PRESSURE: 1860 -74.9924 -29.2823 -147.055 -29.2823 -19.9078 -54.584 -147.055 -54.584 -32.6857
GPRESSURE: 1860 -47.3372 -137.701 -39.9964 -16.3545 64.2436 -51.6532 -186.098 -63.648 34.1783
ENERGY:   1860 1339.4640   3951.2615   2125.0371   281.8235    -309492.9603 26603.1521  0.0000      0.0000      52572.2691  -222619.9530 297.8
946    -42.5286(PRESSURE)    17.0282(GPRESSURE)     859821.2625 -72.3357    -62.8715
PRESSURE: 1870 -48.2164 32.7097 -25.1422 32.7097 -19.5578 131.794 -25.1422 131.794 -189.691
GPRESSURE: 1870 11.8128 69.6595 -16.5929 -31.0603 76.9998 153.058 -13.5146 127.546 -159.561
ENERGY:   1870 1344.7610   3904.3724   2131.2803   269.7844    -309693.7496 26654.1780  0.0000      0.0000      52815.3178  -222574.0555 299.2
718    -85.8218(PRESSURE)    -23.5829(GPRESSURE)    859448.0882 -28.7219    -18.5036
PRESSURE: 1880 67.7263 23.0021 -17.5189 23.0021 104.987 156.01 -17.5189 156.01 26.7902
GPRESSURE: 1880 143.967 15.3178 -29.5841 95.2529 157.447 154.077 39.7776 161.029 103.826
ENERGY:   1880 1395.4111   3907.9728   2130.2727   276.0293    -310295.4807 27081.3588  0.0000      0.0000      52955.0848  -222549.3513 300.0
637    66.5012(PRESSURE)     135.0799(GPRESSURE)    858427.5064 -6.3696     3.6605
***************************************************8

can anybody give me some hint about it?

best regards
wei zhuang