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