AMBER Archive (2008)

Subject: AMBER: Whole System Equilibration & Pressure

From: dpandit_at_brandeis.edu
Date: Mon Apr 14 2008 - 15:57:54 CDT


Hi All:
        After conducting initial 20 PS (protein restrained 5
kcal/mol.A2) constant volume equilibration for target temperature of
310K, I switched to 200 PS constant pressure (unrestrained - whole
system) with pres0 = 1.0. Below are the details. When I checked the
output, temperature and density looks reasonable but I am not sure
about the pressure values as values fluctuate continuously. I have
posted the selected values. Please let me know if I should post those
values in detail. What should I do now? I am not sure what have I done
wrong. Please help.

THX
Deepa

Input File

Stage 2 - Complete System Equilibration/Heating - 200ps MD
  &cntrl imin = 0,
   irest = 1,
   ntx = 7,
   ntb = 2,
   pres0 = 1.0,
   ntp = 1,
   taup = 2.0
   cut = 10,
   ntr = 0,
   ntc = 2,
   ntf = 2,
   tempi = 310.0
   temp0 = 310.0,
   ntt = 3,
   gamma_ln = 1.0,
   nstlim = 100000,
   dt = 0.002,
   ntpr = 100, ntwx = 100, ntwr = 1000,
  /

  summary_avg.PRES summary_rms.PRES

  220.000 -29.9 220.000 201.4

  summary_avg.VOLUME summary_rms.VOLUME
  220.000 301709.6243 220.000 4746.6871

summary_avg.DENSITY summary_rms.DENSITY
220.000 1.0059 220.000 0.0145

summary_avg.TEMP summary_rms.TEMP
  220.000 310.01 220.000 1.78

Selected Pressure Values

      216.000 -218.9
      216.200 102.1
      216.400 2.4
      216.600 -168.3
      216.800 -234.5
      217.000 -310.6
      217.200 -94.9
      217.400 50.2
      217.600 -232.0
      217.800 -117.7
      218.000 -205.4
      218.200 -94.3
      218.400 129.0
      218.600 219.0
      218.800 -271.1
      219.000 45.4
      219.200 47.9
      219.400 65.4
      219.600 -75.4
      219.800 -121.2
      220.000 193.0

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