does it fail for sander (not sander.MPI)?
did you Amber installation pass all of the test cases?
On Sun, May 3, 2020 at 2:05 AM Sunita Patel <sunita.patel.cbs.ac.in> wrote:
> Dear Carlos,
>
> This is the output file after which the simulation stopped. Structure wise
> I didn't see any change.
> Simulation is on a protein with all standard amino acids. As soon as I
> start the NPT, it stops after some steps.
> Kindly please let me know what other files I need to check.
>
> Thanks for your response.
> Sincerely,
> Sunita
>
> ==========pr_npt.out==============
> NSTEP = 5400 TIME(PS) = 1330.800 TEMP(K) = 302.99 PRESS =
> -186.3
> Etot = -69995.8123 EKtot = 17892.6027 EPtot =
> -87888.4150
> BOND = 551.7078 ANGLE = 1406.8705 DIHED =
> 2176.0517
> 1-4 NB = 641.4060 1-4 EEL = 6537.6266 VDWAALS =
> 10690.7561
> EELEC = -109892.8338 EHBOND = 0.0000 RESTRAINT =
> 0.0000
> EKCMT = 7948.2968 VIRIAL = 9313.7679 VOLUME =
> 339464.2715
> Density =
> 0.8694
> Ewald error estimate: 0.1519E-03
>
> ------------------------------------------------------------------------------
>
>
> NSTEP = 5500 TIME(PS) = 1331.000 TEMP(K) = 299.97 PRESS =
> -193.6
> Etot = -69976.4333 EKtot = 17714.4534 EPtot =
> -87690.8867
> BOND = 553.9616 ANGLE = 1437.0462 DIHED =
> 2177.6822
> 1-4 NB = 648.1109 1-4 EEL = 6506.4486 VDWAALS =
> 10591.0509
> EELEC = -109605.1872 EHBOND = 0.0000 RESTRAINT =
> 0.0000
> EKCMT = 7808.3264 VIRIAL = 9225.9895 VOLUME =
> 339189.1719
> Density =
> 0.8701
> Ewald error estimate: 0.3180E-04
>
> ------------------------------------------------------------------------------
>
> On Sat, May 2, 2020 at 4:02 PM Carlos Simmerling <
> carlos.simmerling.gmail.com> wrote:
>
> > People tried to help the last time you posted this, but I don't see where
> > you responded with the info that was requested, or where you checked
> their
> > suggestions
> >
> > On Sat, May 2, 2020, 6:12 AM Sunita Patel <sunita.patel.cbs.ac.in>
> wrote:
> >
> > > Dear Amber users,
> > >
> > > I am still facing the problem during NPT equilibration. Around 5500
> > steps,
> > > the simulation is stopping without any error. I checked it 3 to 4
> times.
> > > For test purpose, I ran NVT with force constant 10 (200 ps) and then
> > with
> > > 1 (200 ps) and then without restraint for 1 ns. During the long
> > > unrestrain NVT, the job ran smoothly. As soon as I started NPT, the job
> > > halted. For a totally different system also the simulation halted
> during
> > > NPT but not during NVT.
> > >
> > > Since there is no error message I am not able to figure out where is
> the
> > > problem.
> > >
> > > Your suggestion will be appreciated.
> > >
> > > Sincerely,
> > > Sunita
> > >
> > > NPT command:
> > > sander.MPI -O -i eq_npt.in -o eq_npt.out -p GSC_D26G_solion.prmtop
> -c
> > > eq_nvt_norst.rst -r eq_npt.rst -x eq_npt.mdcrd -inf eq_npt.info
> > >
> > > Pls have a look on my pr_npt.in file.
> > > ============pr_npt.in=============
> > > Equilibration NPT without restraints 200ps
> > > &cntrl
> > > imin = 0, irest = 1, ntx = 5,
> > > ntb = 2, pres0 = 1.0, ntp = 1,
> > > taup = 2.0,
> > > cut = 10.0, ntr = 0,
> > > ntc = 2, ntf = 2, ig = -1,
> > > tempi = 300.0, temp0 = 300.0,
> > > ntt = 3, gamma_ln = 1.0,
> > > nstlim = 100000, dt = 0.002,
> > > ntpr = 100, ntwx = 100, ntwr = 1000
> > > /
> > > &ewald
> > > order=4,
> > > /
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Received on Sun May 03 2020 - 05:30:02 PDT
