I am sure they took Trump’s advice
Now it’s only a question if this is treason …
On Jul 28, 2016, at 10:44 AM, David Cerutti <dscerutti.gmail.com<mailto:dscerutti.gmail.com>> wrote:
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<mailto: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://urldefense.proofpoint.com/v2/url?u=https-3A__www.dropbox.com_s_18e2297nowsp9dy_TIP4PD.zip-3Fdl-3D0&d=AwIGaQ&c=4R1YgkJNMyVWjMjneTwN5tJRn8m8VqTSNCjYLg1wNX4&r=80h8gfWnXRd-mXPSrw98JBRjhncHe1Sopk2U91C1sZg&m=-HU8qM-pse95C_IFi1To1SNWFrDTeNI0--MzS_UrzBg&s=wck79mQ3wn6YZlcRpfjuV7AcfBLoz8GfEXP23m9m1Kc&e=
TIP4P2005: https://urldefense.proofpoint.com/v2/url?u=https-3A__www.dropbox.com_s_lg3g5oe7tb5i5gq_TIP4P2005.zip-3Fdl-3D0&d=AwIGaQ&c=4R1YgkJNMyVWjMjneTwN5tJRn8m8VqTSNCjYLg1wNX4&r=80h8gfWnXRd-mXPSrw98JBRjhncHe1Sopk2U91C1sZg&m=-HU8qM-pse95C_IFi1To1SNWFrDTeNI0--MzS_UrzBg&s=AJ89a6-6gOrLf-OPX46QSksnY98gwu5P47h-QaImg_0&e=
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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Roman Osman
Department of Structural and Chemical Biology
Mount Sinai School of Medicine
New York, NY 10029
Tel: 212-659-8627
Fax: 212-849-2456
e-mail: roman.osman.mssm.edu<mailto:roman.osman.mssm.edu>
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Received on Thu Jul 28 2016 - 08:30:02 PDT
