AMBER Archive (2008)

Subject: Re: AMBER: temperature spikes

From: Adrian Roitberg (roitberg_at_qtp.ufl.edu)
Date: Sun Jan 06 2008 - 10:41:50 CST

Sally,
Try using irest=1 and ntx=5 when changing temperatures.

That way, you would be reading coordinates and velocities from the
restart file created at the end of the (n-1)th run, and the temperature
at the beginning of the nth run would be the same as the previous one,
but then go to your temp0 value.

Cheers
a.

Sally Pias wrote:
> 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
> -------------
>
>
> ------------------------------------------------------------------------
> 

-- 
                            Dr. Adrian E. Roitberg
                              Associate Professor
               Quantum Theory Project and Department of Chemistry

University of Florida                         PHONE 352 392-6972
P.O. Box 118435                               FAX   352 392-8722
Gainesville, FL 32611-8435                    Email adrian_at_qtp.ufl.edu
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