Dear David,
The 919 and 920 are two water molecules and are surrounded by other water
molecules. I do not see anything strange around this atom.
The solute molecule is quite away from this water molecule.
Thank you for your quick response.
Sincerely,
Sunita
On Sun, Mar 29, 2020 at 10:32 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 - 04:00:02 PDT
