[AMBER] aMD on Amber 12

From: Aldo Segura <asegurac666.yahoo.com.mx>
Date: Tue, 18 Nov 2014 05:53:21 +0000 (UTC)

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no. of atoms: 168207

no. of residues (ligand included): 1491

ave_epot: -510662.9304

ave_dihe: 15864.5125


3.5 * 1491= 5218.5

alphaD = (1/5) * 5218.5 = 1043.7

EthreshD = 5218 + 15864 = 21082

alphaP = 168207 * (1/5) = 33641.4
EthreshP = -510662.9304 + 33641 = -477021.9304



 ig=-1,
  imin=0,irest=1,ntx=5,
  nstlim=125000000,dt=0.002,
  ntc=2,ntf=2,
  cut=8.0, ntb=2, ntp=1, taup=1.0, ioutfm=1, iwrap=1,
  ntpr=5000, ntwx=5000,
  ntt=3, gamma_ln=2.0,
  temp0=300.0,
  iamd=3,
  ethreshd=21082, alphad=1044,
  ethreshp=-477022, alphap=33641,
/

 Here is a fragment ofthe output using pmemd.cuda alone: NSTEP =   815000   TIME(PS) =   2230.000  TEMP(K) =   300.42 PRESS =  -126.8 Etot   =  -406789.1395  EKtot   =   103958.8672  EPtot      =  -510748.0067 BOND   =     4728.6164  ANGLE   =    12275.8411  DIHED      =    15848.4365 1-4 NB =      5330.5300 1-4 EEL =     51522.3414  VDWAALS   =     58875.0408 EELEC  =  -659328.8129  EHBOND  =        0.0000  RESTRAINT  =        0.0000 EKCMT  =    43215.3845  VIRIAL  =    47899.2587  VOLUME     =  1711491.0577                                                   Density    =        1.0067 ------------------------------------------------------------------------------   NSTEP =   820000  TIME(PS) =    2240.000  TEMP(K) =  299.74  PRESS =    90.3 Etot   =  -407887.6661  EKtot   =   103723.1797  EPtot      =  -511610.8458 BOND   =     4629.2373  ANGLE   =    12106.4622  DIHED      =    15802.9587 1-4 NB =      5406.0596 1-4 EEL =     51590.1358  VDWAALS   =     60204.5597 EELEC  =  -661350.2590  EHBOND  =        0.0000  RESTRAINT  =         0.0000 EKCMT  =    43260.6577  VIRIAL  =    39921.4369  VOLUME     =  1712767.3543                                                   Density    =         1.0059 ------------------------------------------------------------------------------  Here is a fragment ofthe output using pmemd.cuda with aMD: NSTEP =   815000   TIME(PS) =   2230.000  TEMP(K) =   301.06 PRESS =   -29.9 Etot   =  -376495.0744  EKtot   =   104180.2891  EPtot      =  -480675.3635 BOND   =     4565.2249  ANGLE   =    13367.1498  DIHED      =    47360.5197 1-4 NB =      5208.1735 1-4 EEL =     50696.1713  VDWAALS   =     59502.2362 EELEC  =  -661374.8389  EHBOND  =        0.0000  RESTRAINT  =        0.0000 EKCMT  =    43190.7528  VIRIAL  =    44297.6105  VOLUME     =  1712793.4145                                                   Density    =         1.0059 ------------------------------------------------------------------------------   NSTEP =   820000  TIME(PS) =    2240.000  TEMP(K) =  300.10  PRESS =     9.4 Etot   =  -377241.0533  EKtot   =   103849.7734  EPtot      =  -481090.8268 BOND   =     4705.3342  ANGLE   =    13608.3724  DIHED      =    47322.2061 1-4 NB =      5160.5467 1-4 EEL =     50426.2493  VDWAALS   =     59466.8915 EELEC  =  -661780.4270  EHBOND  =        0.0000  RESTRAINT  =        0.0000 EKCMT  =    43372.3488  VIRIAL  =    43023.7008  VOLUME     =  1710416.9243                                                   Density    =         1.0073 ------------------------------------------------------------------------------   This is a lastfragment of the amd.log file: bash-4.1$ tail amd.log         5000   785000  -480647.202895273920    47120.363307878375        1.000000000000        0.000172857168        0.000000000000   129716.426811902173        5000   790000  -481134.391026637983    47257.762343714014        1.000000000000        0.000173456921        0.000000000000   129485.995137548394        5000   795000  -480395.602210825775    47564.722687611356        1.000000000000        0.000174808146        0.000000000000   128971.193002039130        5000   800000  -480571.340056136716    47377.097419776954        1.000000000000        0.000173980361        0.000000000000   129285.858609870047        5000   805000  -480442.272442598362    47055.138141021132        1.000000000000        0.000172573546        0.000000000000   129825.815869500351        5000   810000  -479886.118565759622    48143.936395731755        1.000000000000        0.000177401190        0.000000000000   127999.797599786805        5000   815000  -480675.363465000410    47360.519683936611        1.000000000000        0.000173907505        0.000000000000   129313.661078757083        5000   820000  -481090.826785803307    47322.206079091877        1.000000000000        0.000173739297        0.000000000000   129377.916713270373        5000   825000  -480271.830837909132    47518.834657253698        1.000000000000        0.000174605148        0.000000000000   129048.151615417257        5000   830000  -480790.213786629494    47371.100524365902        1.000000000000        0.000173954000        0.000000000000   129295.915984160965 I would appreciate anyhelp with this issue. Best, Aldo =======================================
Aldo Segura-Cabrera
Postdoctoral Fellow
Division of Experimental Hematology and Cancer BiologyCancer and Blood Diseases Institute
Cincinnati Children's Hospital Medical Center
3333 Burnet Ave, MLC 7013, Cincinnati OH 45229
=========================================
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Received on Mon Nov 17 2014 - 22:00:02 PST
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