Dear Carlos,
With sander it has completed 33000 steps and is still running. When I was
using sander.MPI I could run only 5500 steps and after that simulation was
halting.
Could you make out where the problem is?
Kindly pls send your suggestion to fix the problem. It's been a long time I
am facing the issue.
Thank you so much.
Sincerely,
Sunita
On Mon, May 4, 2020 at 12:22 AM Sunita Patel <sunita.patel.cbs.ac.in> wrote:
>
> 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 - 19:00:02 PDT
