Re: [AMBER] Problem During Gradual Heating

From: Carlos Simmerling <carlos.simmerling.gmail.com>
Date: Fri, 28 Jan 2011 09:15:16 -0500

it isn't clear that this is an amber problem.
did you check to see if the job is still running?
does your amber installation pass the test cases?


On Fri, Jan 28, 2011 at 8:58 AM, Hirdesh Kumar <hirdesh.iitd.gmail.com> wrote:
> Hi All,
> I am tying to  heat my system (protein + bound cofactor) slowly. I am using
> ntt =3  with gamma_ln = 1.0, Below mentioned is the script which I am using.
>
>
>
> Heating the system linearly with weak restraints
>  &cntrl
>  imin   = 0,
>  irest  = 0,
>  ntx    = 1,
>  ntb    = 1,
>  cut    = 12,
>  ntr    = 1,
>  ntc    = 2,
>  ntf    = 2,
>  tempi  = 0.0,
>  temp0  = 300.0,
>  ntt    = 3,
>  ig = 20933
>  gamma_ln = 1.0, nmropt=1,
>  nstlim = 50000, dt = 0.002
>  ntpr = 100, ntwx = 100, ntwr = 1000
>  /
>  &wt TYPE='TEMP0', istep1=0, istep2=40000,
>  value1=0.1, value2=300.0, /
>  &wt TYPE='DUMPFREQ',ISTEP1=10, /
>  &wt TYPE='END' /
> Keep protein fixed
> 5.0
> RES 1 339
> END
> END
>
> The equilibration runs fine upto 9100 steps. After that there is* no change
> in the mdout file* but the sander job is running. Previously I didnt
> included Ig value in my script so I thought that it may be due to Ig value
> as I am using ntt=3. Next time I added the Ig value (a random number) but
> this time also the run is upto 7100 steps after that there is no change in
> the mdout file.
>
> Below mentioned is the last line of my output file:
>
>  NSTEP =     7000   TIME(PS) =      14.000  TEMP(K) =    49.27  PRESS =
> 0.0
>  Etot   =   -211822.1441  EKtot   =      5837.1249  EPtot      =
> -217659.2690
>  BOND   =       323.1122  ANGLE   =       956.0308  DIHED      =
> 3200.9235
>  1-4 NB =      1056.0283  1-4 EEL =     14174.4148  VDWAALS    =
> 35009.8809
>  EELEC  =   -272523.6263  EHBOND  =         0.0000  RESTRAINT  =
> 143.9667
>  EAMBER (non-restraint)  =   -217803.2357
>  Ewald error estimate:   0.3030E-04
>  ------------------------------------------------------------------------------
>
>  NMR restraints: Bond =    0.000   Angle =     0.000   Torsion =     0.000
> ===============================================================================
>
>  NSTEP =     7100   TIME(PS) =      14.200  TEMP(K) =    50.36  PRESS =
> 0.0
>  Etot   =   -211664.7202  EKtot   =      5966.1111  EPtot      =
> -217630.8314
>  BOND   =       312.2514  ANGLE   =       957.5403  DIHED      =
> 3192.0819
>  1-4 NB =      1062.4902  1-4 EEL =     14166.2999  VDWAALS    =
> 34826.4805
>  EELEC  =   -272299.1537  EHBOND  =         0.0000  RESTRAINT  =
> 151.1782
>  EAMBER (non-restraint)  =   -217782.0095
>  Ewald error estimate:   0.2147E-04
>  ------------------------------------------------------------------------------
>
>  NMR restraints: Bond =    0.000   Angle =     0.000   Torsion =     0.000
> ===============================================================================
>
>
>
> Please suggest me where I am wrong..
>
> Thanks
> Hirdesh
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>

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Received on Fri Jan 28 2011 - 06:30:05 PST
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