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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>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>>
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Received on Fri Jan 28 2011 - 06:30:09 PST
