[AMBER] Solute and solvent temperatures in mden

From: Mickey Richards <mickey18385.gmail.com>
Date: Thu, 10 Jun 2010 16:45:35 -0600

I am comparing the Berendsen thermostat (ntt = 1) to Langevin dynamics (ntt
= 3), for a long simulation (250 ns) of a carbohydrate in explicit TIP3P
water in AMBER10, using PMEMD, and GLYCAM06. When I look at the mden file
generated during my simulations, the temperature for the system and the
solute are the same, and the temperature for the solvent takes on values of
-0.2675E+10. These values are similar for both temperature regulation

1) Are these negative values for the solvent temperature typical?

2) Is there a way to interrogate whether the solute and solvent are both
holding their temperatures appropriately.

The first few lines of the mden file are below my signature. Thank you.

With best regards,
--Mickey Richards
Department of Chemistry
University of Alberta
email:  mickey18385.gmail.com
L0  Nsteps           time(ps)         Etot             EKinetic
L1  Temp             T_solute         T_solv           Pres_scal_solu
L2  Pres_scal_solv   BoxX             BoxY             BoxZ
L3  volume           pres_X           pres_Y           pres_Z
L4  Pressure         EKCoM_x          EKCoM_y          EKCoM_z
L5  EKComTot         VIRIAL_x         VIRIAL_y         VIRIAL_z
L6  VIRIAL_tot       E_pot            E_vdw            E_el
L7  E_hbon           E_bon            E_angle          E_dih
L8  E_14vdw          E_14el           E_const          E_pol
L9  AV_permMoment    AV_indMoment     AV_totMoment     Density
L0     1000  0.3020000000E+03  -.2143942587E+04  0.5315329511E+03
L1 0.2940950593E+03  0.2940950593E+03  -.2675475538E+10  0.1000000000E+01
L2 0.1000000000E+01  0.2208616238E+02  0.2084443822E+02  0.2007675642E+02
L3 0.9240859493E+04  -.3447777733E+02  0.8924758727E+03  -.1452598248E+03
L4 0.2375794235E+03  0.7699423012E+02  0.8707555144E+02  0.7811022865E+02
L5 0.2421800102E+03  0.7928725205E+02  0.2771944143E+02  0.8777105916E+02
L6 0.1947777526E+03  -.2675475538E+04  0.4321782932E+03  -.3334556462E+04
L7 0.0000000000E+00  0.6436629656E+01  0.1133669567E+02  0.1359157121E+02
L8 0.3126971760E+01  0.1924107619E+03  0.0000000000E+00  0.0000000000E+00
L9 0.0000000000E+00  0.0000000000E+00  0.0000000000E+00  0.9802280553E+00
L0     2000  0.3040000000E+03  -.2122444637E+04  0.5329041341E+03
L1 0.2948537294E+03  0.2948537294E+03  -.2655348771E+10  0.1000000000E+01
L2 0.1000000000E+01  0.2208742050E+02  0.2084562561E+02  0.2007790008E+02
L3 0.9244586023E+04  -.4159032492E+03  0.1635469145E+04  -.1288171800E+04
L4 -.2286863481E+02  0.8037102083E+02  0.1006596462E+03  0.8454745358E+02
L5 0.2655781206E+03  0.1080427540E+03  -.8154761619E+01  0.1702547579E+03
L6 0.2701427502E+03  -.2655348771E+04  0.4046798114E+03  -.3281952483E+04
L7 0.0000000000E+00  0.2426956117E+01  0.1440711111E+02  0.1050531178E+02
L8 0.2587346814E+01  0.1919971750E+03  0.0000000000E+00  0.0000000000E+00
L9 0.0000000000E+00  0.0000000000E+00  0.0000000000E+00  0.9798329214E+00
L0     3000  0.3060000000E+03  -.2181139283E+04  0.5285750245E+03
L1 0.2924584503E+03  0.2924584503E+03  -.2709714308E+10  0.1000000000E+01
L2 0.1000000000E+01  0.2201347493E+02  0.2077583739E+02  0.2001068209E+02
L3 0.9152007356E+04  0.4132042301E+03  -.1257837691E+02  -.4543696533E+03
L4 -.1791460005E+02  0.8323863846E+02  0.8595059140E+02  0.8147895890E+02
L5 0.2506681888E+03  0.5602179851E+02  0.8677910100E+02  0.1114072734E+03
L6 0.2542081729E+03  -.2709714308E+04  0.4120169489E+03  -.3345113772E+04
L7 0.0000000000E+00  0.5266836046E+01  0.1464807540E+02  0.9461897526E+01
L8 0.1523550182E+01  0.1924821561E+03  0.0000000000E+00  0.0000000000E+00
L9 0.0000000000E+00  0.0000000000E+00  0.0000000000E+00  0.9897445858E+00
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Received on Thu Jun 10 2010 - 16:00:03 PDT
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