I'm posing this question because of a general problem I've encountered doing several molecular dynamics simulations, but also out of general interest: The initial temperature in a MD calculation must be related to the average velocity of the atomic nuclei at the beginning of the MD run. Using the log2egy script for my simulations (free molecular dynamics of an Au12-cluster with an initial temperature of 1000 K) I see a much higher "temperature" or kinetic energy for the first few steps of the simulation:
# mdlog[.1-last] used as log with 0 constraints
# t= KineticE= TotalE= PotentialE= P(GPa)= T(K)= xi=
0.00 0.0678886262 -1629.6569633338 -1629.7248519600 0.0000000000 1429.0386836096 0.0000000000
80.00 0.0678035727 -1629.6569624073 -1629.7247659800 0.0000000000 1427.2483290876 0.0000000000
160.00 0.0675490601 -1629.6569611999 -1629.7245102600 0.0000000000 1421.8909012051 0.0000000000
240.00 0.0671257329 -1629.6569616371 -1629.7240873700 0.0000000000 1412.9799691474 0.0000000000
320.00 0.0665353768 -1629.6569616832 -1629.7234970600 0.0000000000 1400.5531193079 0.0000000000
400.00 0.0657822655 -1629.6569635045 -1629.7227457700 0.0000000000 1384.7003147275 0.0000000000
480.00 0.0648708263 -1629.6569631737 -1629.7218340000 0.0000000000 1365.5147473798 0.0000000000
560.00 0.0638092959 -1629.6569691541 -1629.7207784500 0.0000000000 1343.1697959311 0.0000000000
640.00 0.0626074696 -1629.6569710204 -1629.7195784900 0.0000000000 1317.8716516750 0.0000000000
720.00 0.0612744206 -1629.6569721494 -1629.7182465700 0.0000000000 1289.8113021776 0.0000000000
800.00 0.0598217024 -1629.6569756376 -1629.7167973400 0.0000000000 1259.2319459042 0.0000000000
880.00 0.0582626752 -1629.6569788648 -1629.7152415400 0.0000000000 1226.4148098113 0.0000000000
960.00 0.0566116467 -1629.6569792533 -1629.7135909000 0.0000000000 1191.6610720954 0.0000000000
1040.00 0.0548856872 -1629.6569868128 -1629.7118725000 0.0000000000 1155.3300535506 0.0000000000
1120.00 0.0531025860 -1629.6569896140 -1629.7100922000 0.0000000000 1117.7962174187 0.0000000000
1200.00 0.0512783891 -1629.6569896809 -1629.7082680700 0.0000000000 1079.3973266416 0.0000000000
1280.00 0.0494322474 -1629.6569966026 -1629.7064288500 0.0000000000 1040.5365040216 0.0000000000
1360.00 0.0475829837 -1629.6569994863 -1629.7045824700 0.0000000000 1001.6099623209 0.0000000000
1440.00 0.0457476143 -1629.6570005057 -1629.7027481200 0.0000000000 962.9758929136 0.0000000000
1520.00 0.0439448765 -1629.6570065635 -1629.7009514400 0.0000000000 925.0287123615 0.0000000000
1600.00 0.0421921294 -1629.6570093606 -1629.6992014900 0.0000000000 888.1338206688 0.0000000000
1680.00 0.0405041719 -1629.6570117781 -1629.6975159500 0.0000000000 852.6027357919 0.0000000000
1760.00 0.0388952937 -1629.6570153263 -1629.6959106200 0.0000000000 818.7362500605 0.0000000000
1840.00 0.0373779111 -1629.6570180389 -1629.6943959500 0.0000000000 786.7957244524 0.0000000000
1920.00 0.0359624365 -1629.6570216535 -1629.6929840900 0.0000000000 757.0003375180 0.0000000000
2000.00 0.0346571164 -1629.6570249036 -1629.6916820200 0.0000000000 729.5236743856 0.0000000000
2080.00 0.0334681044 -1629.6570286156 -1629.6904967200 0.0000000000 704.4952669487 0.0000000000
2160.00 0.0323998262 -1629.6570323038 -1629.6894321300 0.0000000000 682.0082776904 0.0000000000
2240.00 0.0314541591 -1629.6570355509 -1629.6884897100 0.0000000000 662.1022203530 0.0000000000
2320.00 0.0306306389 -1629.6570385811 -1629.6876692200 0.0000000000 644.7673240441 0.0000000000
2400.00 0.0299274750 -1629.6570421050 -1629.6869695800 0.0000000000 629.9658998663 0.0000000000
2480.00 0.0293408394 -1629.6570447206 -1629.6863855600 0.0000000000 617.6173652700 0.0000000000
2560.00 0.0288661188 -1629.6570487112 -1629.6859148300 0.0000000000 607.6246151327 0.0000000000
2640.00 0.0284976464 -1629.6570512736 -1629.6855489200 0.0000000000 599.8683630177 0.0000000000
2720.00 0.0282281463 -1629.6570534637 -1629.6852816100 0.0000000000 594.1954529022 0.0000000000
2800.00 0.0280502705 -1629.6570551495 -1629.6851054200 0.0000000000 590.4512129856 0.0000000000
2880.00 0.0279560585 -1629.6570567715 -1629.6850128300 0.0000000000 588.4680724469 0.0000000000
2960.00 0.0279375700 -1629.6570575800 -1629.6849951500 0.0000000000 588.0788944965 0.0000000000
3040.00 0.0279869123 -1629.6570580877 -1629.6850450000 0.0000000000 589.1175385789 0.0000000000
3120.00 0.0280959955 -1629.6570580845 -1629.6851540800 0.0000000000 591.4137121447 0.0000000000
3200.00 0.0282577147 -1629.6570575853 -1629.6853153000 0.0000000000 594.8178597939 0.0000000000
3280.00 0.0284655344 -1629.6570571756 -1629.6855227100 0.0000000000 599.1924132971 0.0000000000
3360.00 0.0287127635 -1629.6570557165 -1629.6857684800 0.0000000000 604.3965238673 0.0000000000
3440.00 0.0289933694 -1629.6570539006 -1629.6860472700 0.0000000000 610.3032080052 0.0000000000
3520.00 0.0293023196 -1629.6570518204 -1629.6863541400 0.0000000000 616.8065346237 0.0000000000
3600.00 0.0296347846 -1629.6570491054 -1629.6866838900 0.0000000000 623.8048393778 0.0000000000
3680.00 0.0299867357 -1629.6570460543 -1629.6870327900 0.0000000000 631.2133230674 0.0000000000
3760.00 0.0303547474 -1629.6570429526 -1629.6873977000 0.0000000000 638.9598769432 0.0000000000
3840.00 0.0307357068 -1629.6570390632 -1629.6877747700 0.0000000000 646.9789765632 0.0000000000
3920.00 0.0311267557 -1629.6570351243 -1629.6881618800 0.0000000000 655.2104593077 0.0000000000
4000.00 0.0315251039 -1629.6570312461 -1629.6885563500 0.0000000000 663.5955904624 0.0000000000
4080.00 0.0319285685 -1629.6570277515 -1629.6889563200 0.0000000000 672.0884186227 0.0000000000
4160.00 0.0323353854 -1629.6570243246 -1629.6893597100 0.0000000000 680.6518148695 0.0000000000
4240.00 0.0327439064 -1629.6570217636 -1629.6897656700 0.0000000000 689.2510795028 0.0000000000
4320.00 0.0331518674 -1629.6570190426 -1629.6901709100 0.0000000000 697.8385566017 0.0000000000
4400.00 0.0335575666 -1629.6570164934 -1629.6905740600 0.0000000000 706.3784231253 0.0000000000
4480.00 0.0339576985 -1629.6570147115 -1629.6909724100 0.0000000000 714.8011002347 0.0000000000
4560.00 0.0343507231 -1629.6570153169 -1629.6913660400 0.0000000000 723.0741699052 0.0000000000
4640.00 0.0347353197 -1629.6570143403 -1629.6917496600 0.0000000000 731.1698338985 0.0000000000
4720.00 0.0351074200 -1629.6570142300 -1629.6921216500 0.0000000000 739.0024514940 0.0000000000
4800.00 0.0354646880 -1629.6570145720 -1629.6924792600 0.0000000000 746.5228540473 0.0000000000
4880.00 0.0358037640 -1629.6570150560 -1629.6928188200 0.0000000000 753.6603193542 0.0000000000
4960.00 0.0361214322 -1629.6570165378 -1629.6931379700 0.0000000000 760.3471560523 0.0000000000
5040.00 0.0364148006 -1629.6570177594 -1629.6934325600 0.0000000000 766.5224891204 0.0000000000
5120.00 0.0366803773 -1629.6570190027 -1629.6936993800 0.0000000000 772.1128120426 0.0000000000
5200.00 0.0369146950 -1629.6570206450 -1629.6939353400 0.0000000000 777.0451408313 0.0000000000
5280.00 0.0371140596 -1629.6570221504 -1629.6941362100 0.0000000000 781.2417154579 0.0000000000
5360.00 0.0372758183 -1629.6570247717 -1629.6943005900 0.0000000000 784.6466971509 0.0000000000
5440.00 0.0373973085 -1629.6570265915 -1629.6944239000 0.0000000000 787.2040350057 0.0000000000
5520.00 0.0374754330 -1629.6570283570 -1629.6945037900 0.0000000000 788.8485354867 0.0000000000
5600.00 0.0375078737 -1629.6570302363 -1629.6945381100 0.0000000000 789.5314059908 0.0000000000
5680.00 0.0374928307 -1629.6570319293 -1629.6945247600 0.0000000000 789.2147537242 0.0000000000
5760.00 0.0374286569 -1629.6570333831 -1629.6944620400 0.0000000000 787.8639108754 0.0000000000
5840.00 0.0373141520 -1629.6570346380 -1629.6943487900 0.0000000000 785.4536119668 0.0000000000
5920.00 0.0371490136 -1629.6570357064 -1629.6941847200 0.0000000000 781.9774897077 0.0000000000
6000.00 0.0369332946 -1629.6570361254 -1629.6939694200 0.0000000000 777.4366587877 0.0000000000
6080.00 0.0366681204 -1629.6570363896 -1629.6937045100 0.0000000000 771.8548081399 0.0000000000
6160.00 0.0363547744 -1629.6570359356 -1629.6933907100 0.0000000000 765.2589522002 0.0000000000
6240.00 0.0359949530 -1629.6570345570 -1629.6930295100 0.0000000000 757.6848017134 0.0000000000
6320.00 0.0355908798 -1629.6570328002 -1629.6926236800 0.0000000000 749.1791598960 0.0000000000
6400.00 0.0351459361 -1629.6570310739 -1629.6921770100 0.0000000000 739.8132071590 0.0000000000
6480.00 0.0346642034 -1629.6570282566 -1629.6916924600 0.0000000000 729.6728530875 0.0000000000
6560.00 0.0341498429 -1629.6570248271 -1629.6911746700 0.0000000000 718.8456930862 0.0000000000
6640.00 0.0336074214 -1629.6570205386 -1629.6906279600 0.0000000000 707.4278559755 0.0000000000
6720.00 0.0330411817 -1629.6570157083 -1629.6900568900 0.0000000000 695.5086495680 0.0000000000
6800.00 0.0324572655 -1629.6570118345 -1629.6894691000 0.0000000000 683.2173591887 0.0000000000
6880.00 0.0318610242 -1629.6570059558 -1629.6888669800 0.0000000000 670.6666279330 0.0000000000
6960.00 0.0312576654 -1629.6570014246 -1629.6882590900 0.0000000000 657.9660757749 0.0000000000
Afterwards the kinetic energy of the nuclei drops quite quickly and severely. The total energy oscillates but stays constant for the whole of the simulation. This drop of the kinetic energy (to me) seems reasonable, even though it is quite large. What I don't understand is why the inital temperature is so much higher than the 1000 K I want it to be. How are the initial velocities generated? Especially with respect to the initial temperature from the user's input in mdprep?
Thanks a lot for any help with this question.
Linn