Hi it seems that your system will take some more time to converge.
You can take the restart file generated in your simulation and gain continue it for more 2000-3000 steps.
You will have to do it until you energy converge.
with regards,
AT
________________________________
From: Suguru ASAI <suguruasai.gmail.com>
Sent: Thursday, July 28, 2016 4:15:55 AM
To: amber.ambermd.org
Subject: Re: [AMBER] EEL become ****** in minimization
Dear Dave,
That's scared at least if they can find my project detail from such
practice simulations ;-)
Anyway, thanks for replay.
> 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've noticed as well but I also saw "****" in VDWAALS on TIP4P/2005 and
even an original TIP4P so I thought it is a kind feature of TIP4P... So
could you give me a way to fix this? I've visually checked the O569 and
H570 but I couldn't find any difference from others...
https://urldefense.proofpoint.com/v2/url?u=https-3A__www.dropbox.com_s_biqsnf8iy17ynxx_569-5F570.png-3Fdl-3D0&d=CwIGaQ&c=y2w-uYmhgFWijp_IQN0DhA&r=0Hah93XWYYBgmROOVcaccg&m=5IV_h0yRdDx3C2wUrC8mWWBI1NQ6yG1vbuIzAIfKGK0&s=jvg5_-_aaKQH2nzb5-eyGkI6fnMKRKww1ZN7vIIx9oQ&e=
Thanks for your help.
Asai
On 7/28/16 23:44, David Cerutti 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> 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=CwIGaQ&c=y2w-uYmhgFWijp_IQN0DhA&r=0Hah93XWYYBgmROOVcaccg&m=5IV_h0yRdDx3C2wUrC8mWWBI1NQ6yG1vbuIzAIfKGK0&s=svfXF2Y4nXRW4UdDqRjyca5vToeRTT0tGthv6pHsLU8&e=
>> TIP4P2005: https://urldefense.proofpoint.com/v2/url?u=https-3A__www.dropbox.com_s_lg3g5oe7tb5i5gq_TIP4P2005.zip-3Fdl-3D0&d=CwIGaQ&c=y2w-uYmhgFWijp_IQN0DhA&r=0Hah93XWYYBgmROOVcaccg&m=5IV_h0yRdDx3C2wUrC8mWWBI1NQ6yG1vbuIzAIfKGK0&s=O2Cr6IognsXc2tUNz8_XhKjxI0wvxyHp_2Sg5wJ7UYw&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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Received on Thu Jul 28 2016 - 12:00:02 PDT
