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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> >
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Received on Sat May 02 2020 - 23:30:02 PDT
