The AMBER14 installation passed all the tests. I started the run with
sander for testing and will let you know if it crashes.
Thank you so much Carlos.
Sincerely,
Sunita
On Sun, May 3, 2020 at 5:47 PM Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> 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 - 12:00:02 PDT
