Hi,
did you solve the issue? If atom 920 is part of the solvent I guess you are
modelling a small molecule. As Carlos Simmerling asked before, are you
using new parameters in the description of this solute?
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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Received on Mon Mar 30 2020 - 00:00:02 PDT
