AMBER Archive (2008)

Subject: RE: AMBER: Whole System Equilibration & Pressure

From: dpandit_at_brandeis.edu
Date: Tue Apr 15 2008 - 09:16:35 CDT

Hi Ross,
         Thank you for your explanation.

I calculated pressure average for last 120 PS and it came out to be
-33.4267. I also calculated potential energy for the same time window
and it comes to -90450.02666 kcal/mol.

When I checked the potential energy for last 20 PS (data below). I
feel it is stable but again pressure is not. Is it OK to go ahead with
production run or may be I should run Equilibration for additional 100
or more PS.

You must have got a sense but just to be clear this is my first run on
my own protein system and just want to be sure I do each step properly.

THX
Deepa

Last 20 PS

Time EPTOT Pressure

200.000 -90332.2068 -88.0
200.200 -90351.6764 -204.1
200.400 -90472.9897 -84.1
200.600 -90548.8745 208.8
200.800 -90529.7328 -84.5
201.000 -90407.9667 -154.0
201.200 -90461.9499 -66.1
201.400 -90524.0491 90.3
201.600 -90592.2800 127.2
201.800 -90584.9101 -13.8
202.000 -90661.8926 -9.4
202.200 -90572.2363 89.5
202.400 -90284.7273 161.8
202.600 -90462.4058 -35.5
202.800 -90477.4392 140.8
203.000 -90171.9316 199.6
203.200 -90161.2672 -13.2
203.400 -90422.9096 -233.9
203.600 -90439.8612 19.6
203.800 -90403.6969 -20.2
204.000 -90508.8114 85.5
204.200 -90622.2453 151.8
204.400 -90518.9924 -100.6
204.600 -90595.2169 -6.0
204.800 -90600.4676 -207.5
205.000 -90608.2456 57.9
205.200 -90507.7104 22.5
205.400 -90399.8538 131.3
205.600 -90369.1100 -5.3
205.800 -90520.0574 15.9
206.000 -90602.7546 -167.7
206.200 -90463.9826 124.6
206.400 -90330.6453 -210.4
206.600 -90579.3700 137.2
206.800 -90632.7462 -165.6
207.000 -90382.7873 -108.2
207.200 -90468.9429 184.6
207.400 -90364.7291 -301.7
207.600 -90266.5077 141.2
207.800 -90520.4553 204.9
208.000 -90514.7037 -46.4
208.200 -90417.0059 90.7
208.400 -90466.4572 23.9
208.600 -90542.2463 -35.4
208.800 -90289.0341 245.7
209.000 -90414.2091 -185.9
209.200 -90519.2059 -190.2
209.400 -90540.7489 25.3
209.600 -90452.0413 43.5
209.800 -90471.0041 -145.3
210.000 -90594.9235 -91.8
210.200 -90530.7243 -97.8
210.400 -90597.4833 93.0
210.600 -90493.5695 257.2
210.800 -90388.6438 161.5
211.000 -90476.3032 -196.4
211.200 -90383.7622 208.0
211.400 -90619.8912 141.9
211.600 -90645.2119 -64.9
211.800 -90692.0464 -94.8
212.000 -90660.8265 51.4
212.200 -90608.9304 60.7
212.400 -90397.1957 -193.0
212.600 -90523.3182 -39.8
212.800 -90364.2632 -199.0
213.000 -90514.1676 110.0
213.200 -90390.1909 -5.0
213.400 -90360.9160 -26.5
213.600 -90407.8198 87.7
213.800 -90402.8127 -35.8
214.000 -90350.5548 251.7
214.200 -90493.9525 148.1
214.400 -90384.5143 64.3
214.600 -90518.7841 -288.3
214.800 -90462.1285 39.1
215.000 -90467.0568 -92.1
215.200 -90476.5881 -115.4
215.400 -90558.0333 -128.4
215.600 -90371.8993 -82.6
215.800 -90487.3594 -148.5
216.000 -90475.1532 -218.9
216.200 -90541.0612 102.1
216.400 -90561.1378 2.4
216.600 -90631.2679 -168.3
216.800 -90601.1844 -234.5
217.000 -90640.3871 -310.6
217.200 -90593.5781 -94.9
217.400 -90529.2429 50.2
217.600 -90519.3891 -232.0
217.800 -90523.3637 -117.7
218.000 -90498.7772 -205.4
218.200 -90267.2011 -94.3
218.400 -90239.5129 129.0
218.600 -90341.5466 219.0
218.800 -90326.9296 -271.1
219.000 -90561.0405 45.4
219.200 -90509.0286 47.9
219.400 -90491.8796 65.4
219.600 -90519.7269 -75.4
219.800 -90621.1018 -121.2
220.000 -90612.2134 193.0

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