Asai, the Russians have hacked into your simulation and the missing numbers
will be published on Wikileaks if Julian Assange has a personal vendetta
against you.
Before the "****" in EEL, however, I see that there are "****" in VDWAALS.
There was a terrible vdW clash in your simulation at the beginning. I
would see about removing this before proceeding with minimization; you
might be able to detect the clash by simple visualization (from the output
it seems to involve atom O 569, which is probably water given that the
problem then migrates to H1 570).
Dave
On Thu, Jul 28, 2016 at 10:04 AM, Suguru ASAI <suguruasai.gmail.com> wrote:
> Dear AMBER users,
>
> # Summary
>
> EEL value in mdout become ******* in minimization and a program failed.
> I would like to solve this problem but don't know where to check or how
> to fix.
>
>
> # Detail
>
> I've tried to use TIP4P-D water model (1) which is derived from
> TIP4P/2005 water model (2).
> So I've created frcmod and off files of both water models and performed
> water only simulations.
> However, EEL values in a simulation of TIP4P-D became ********** within
> 100 steps like:
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1 4.7263E+08 2.1830E+08 6.9776E+09 O 569
>
> BOND = 0.1578 ANGLE = 0.0000 DIHED = 0.0000
> VDWAALS = ************* EEL = 737.3763 HBOND = 0.0000
> 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 100 -1.1110E+08 1.1744E+12 4.3130E+13 H1 570
>
> BOND = 970.3621 ANGLE = 0.0000 DIHED = 0.0000
> VDWAALS = 2936.1737 EEL = ************* HBOND = 0.0000
> 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT =
> 1016.3076
> EAMBER = *************
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 200 -6.1725E+08 3.6244E+13 1.3291E+15 H1 570
>
> BOND = 970.3620 ANGLE = 0.0000 DIHED = 0.0000
> VDWAALS = 2936.1736 EEL = ************* HBOND = 0.0000
> 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT =
> 1016.3076
> EAMBER = *************
>
> And sander/pmemd showed SEGV and stopped.
> It did not happen with TIP4P/2005 and the differences between TIP4P-D
> and TIP4P/2005 are
>
> - ACOEFF (TIP4PD: 9.04E+05, TIP4P2005: 7.31E+05; Found in prmtop file)
> - BCOEFF (TIP4PD: 8.99E+02, TIP4P2005: 7.36E+02; Found in prmtop file)
> - HW charge (TIP4PD: 0.58, TIP4P2005: 0.5564; Written in OFF file)
>
> So I'm guessing relatively large ACOEFF/BCOEFF of TIP4P-D would cause
> the issue but I don't really know if it is or way to fix.
> So I would be grateful if someone give me a direction to solve this.
>
> In case if you need more details, I uploaded parameter files (frcmod,
> off, PDBs) I used on
>
> TIP4PD: https://www.dropbox.com/s/18e2297nowsp9dy/TIP4PD.zip?dl=0
> TIP4P2005: https://www.dropbox.com/s/lg3g5oe7tb5i5gq/TIP4P2005.zip?dl=0
>
>
> Thanks for reading.
>
>
> Asai
>
>
> 1. Piana S, Donchev AG, Robustelli P, Shaw DE (2015) Water Dispersion
> Interactions Strongly Influence Simulated Structural Properties of
> Disordered Protein States. J Phys Chem B 119: 5113–5123.
> 2. Abascal JLF, Vega C (2005) A general purpose model for the condensed
> phases of water: TIP4P/2005. J Chem Phys 123: 234505.
>
>
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Received on Thu Jul 28 2016 - 08:00:02 PDT
