[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
schemes.

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
dV/dlambda
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
0.0000000000E+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
0.0000000000E+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
0.0000000000E+00
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Received on Thu Jun 10 2010 - 16:00:03 PDT
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