Re: [AMBER] Problem During Gradual Heating

From: Carlos Simmerling <carlos.simmerling.gmail.com>
Date: Fri, 28 Jan 2011 09:23:25 -0500

try running it single processor as a test- sometimes if there is an
error message on one of the non-master nodes it won't go in the output
file.



On Fri, Jan 28, 2011 at 9:18 AM, Hirdesh Kumar <hirdesh.iitd.gmail.com> wrote:
> Yes, I checked for job status. and I found that it is still running. I think
> that the amber installation in OK as all other jobs are running OK. I am
> runnning the job using MPI.
>
>
>
> On Fri, Jan 28, 2011 at 7:45 PM, Carlos Simmerling <
> carlos.simmerling.gmail.com> wrote:
>
>> 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 - 06:30:09 PST
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