AMBER Archive (2008)

Subject: AMBER: temperature spikes

From: Sally Pias (sallypias_at_gmail.com)
Date: Sun Jan 06 2008 - 00:26:55 CST

I am attempting to equilibrate an NMR-based model of a 120-residue
protein domain. After minimizing the system, I first carried out a
constant volume, constant temperature equilibration run for 1
nanosecond at 100 K. I then raised the temperature (with constant
volume) in stages of 50 K per 25 picoseconds, reaching 300 K after 100
picoseconds. While heating the system up, I found that the
temperature would spike at the beginning of each stage but would then
return to a value near that specified as tempi. Is there a problem
with the protocol I am using (which I developed by combining
information from two tutorials)?

Here is the first of my input files for heating the system up. The
others change only tempi and temp0:
------------
Equilibration stage 2: Heating the system up to 150K with constant volume
 &cntrl
   nstlim=12500, dt=0.002, ntx=1, irest=0, ntpr=500, ntwr=2500, ntwx=2500,

   tempi=100.0, temp0=150.0, ntt=1, tautp=2.0, ig=209858,

   ntb=1, ntp=0,

   ntc=2, ntf=2,

   nrespa=2,
 &end
-------------

Attached is a graph showing the output temperature data.
The data are also given below for each stage, with temperature spikes noted:
-------------
1000.000 145.41 ## spike
1001.000 110.44
1002.000 118.55
1003.000 125.58
1004.000 131.07
1005.000 132.68
1006.000 136.76
1007.000 139.69
1008.000 140.73
1009.000 144.12
1010.000 143.15
1011.000 144.33
1012.000 146.90
1013.000 146.17
1014.000 147.25
1015.000 147.89
1016.000 148.52
1017.000 148.30
1018.000 149.69
1019.000 148.35
1020.000 149.50
1021.000 149.34
1022.000 149.08
1023.000 150.01
1024.000 147.63
1025.000 150.31
-----
1025.000 218.12 ## spike
1026.000 159.12
1027.000 168.22
1028.000 172.53
1029.000 176.73
1030.000 184.60
1031.000 183.52
1032.000 186.15
1033.000 190.25
1034.000 190.96
1035.000 191.66
1036.000 193.87
1037.000 195.68
1038.000 194.20
1039.000 195.11
1040.000 197.22
1041.000 196.79
1042.000 196.35
1043.000 198.68
1044.000 198.22
1045.000 196.68
1046.000 196.77
1047.000 200.92
1048.000 199.62
1049.000 198.48
1050.000 198.12
-----
1050.000 290.83 ## spike
1051.000 208.91
1052.000 215.69
1053.000 217.75
1054.000 223.33
1055.000 228.08
1056.000 231.37
1057.000 233.06
1058.000 231.88
1059.000 235.84
1060.000 238.07
1061.000 236.28
1062.000 240.82
1063.000 241.39
1064.000 242.18
1065.000 243.16
1066.000 244.21
1067.000 247.92
1068.000 248.27
1069.000 246.41
1070.000 246.80
1071.000 245.54
1072.000 247.32
1073.000 250.13
1074.000 248.09
1075.000 250.10
-----
1075.000 363.53 ## spike
1076.000 258.02
1077.000 264.42
1078.000 269.01
1079.000 276.42
1080.000 274.87
1081.000 279.61
1082.000 280.70
1083.000 287.64
1084.000 289.46
1085.000 289.64
1086.000 291.01
1087.000 290.01
1088.000 294.59
1089.000 293.38
1090.000 290.16
1091.000 292.53
1092.000 297.89
1093.000 294.78
1094.000 294.83
1095.000 298.67
1096.000 295.40
1097.000 297.00
1098.000 297.36
1099.000 299.75
1100.000 302.28
-------------


temp_duan_eq2_all.jpg -----------------------------------------------------------------------
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