Do you perhaps have a small molecule or other part for which you loaded new
parameters? That's what I would suspect first.
It's hard to say much without knowing more about your setup.
On Sun, Mar 29, 2020, 1:01 AM David Sáez <davidsaez.udec.cl> wrote:
> Hi,
>
> Usually the first step is taking a look at at or around the atoms involved
> ( 919 and 920). Do you see anything strange in there?
>
> David.
>
> On Sun, Mar 29, 2020 at 1:11 AM Sunita Patel <sunita.patel.cbs.ac.in>
> wrote:
>
> > Dear Users,
> >
> > When I am doing NPT equilibration, I am getting the message " Coordinate
> > resetting (SHAKE) cannot be accomplished" and after that the calculation
> is
> > stopped.
> >
> > I finished position restraint NVT without any problem. My pr_NTP.in file
> is
> > shown below. The pr_npt.out file's output is given below. I tried
> > resubmitting the job several times but getting the same message at the
> same
> > step number 800.
> >
> > How can I rectify this?
> >
> > Thanks in advance.
> >
> > Sincerely,
> > Sunita
> >
> > ----------------------------pr_NPT.in--------
> > &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,
> > /
> > -----------------------------
> > NSTEP = 700 TIME(PS) = 21.400 TEMP(K) = 300.17 PRESS =
> > -218.5
> > Etot = -74699.8208 EKtot = 19122.0076 EPtot =
> > -93821.8284
> > BOND = 544.7494 ANGLE = 1427.3090 DIHED =
> > 2223.9704
> > 1-4 NB = 661.6464 1-4 EEL = 6471.0812 VDWAALS =
> > 11607.7526
> > EELEC = -116758.3373 EHBOND = 0.0000 RESTRAINT =
> > 0.0000
> > EKCMT = 8577.8177 VIRIAL = 10409.9257 VOLUME =
> > 388345.7996
> > Density =
> > 0.8201
> > Ewald error estimate: 0.9435E-04
> >
> >
> ------------------------------------------------------------------------------
> >
> >
> > NSTEP = 800 TIME(PS) = 21.600 TEMP(K) = 298.98 PRESS =
> > -326.6
> > Etot = -74794.7684 EKtot = 19046.3671 EPtot =
> > -93841.1355
> > BOND = 575.3748 ANGLE = 1400.1912 DIHED =
> > 2225.2308
> > 1-4 NB = 633.8584 1-4 EEL = 6453.8437 VDWAALS =
> > 11479.9745
> > EELEC = -116609.6089 EHBOND = 0.0000 RESTRAINT =
> > 0.0000
> > EKCMT = 8477.3787 VIRIAL = 11210.5540 VOLUME =
> > 387619.0198
> > Density =
> > 0.8216
> > Ewald error estimate: 0.7500E-04
> >
> >
> ------------------------------------------------------------------------------
> >
> > vlimit exceeded for step 816; vmax = 28847.4477
> >
> > Coordinate resetting (SHAKE) cannot be accomplished,
> > deviation is too large
> > NITER, NIT, LL, I and J are : 0 0 436 919 920
> >
> > Note: This is usually a symptom of some deeper
> > problem with the energetics of the system.
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> >
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Received on Sun Mar 29 2020 - 03:30:02 PDT
