Re: [AMBER] EEL become ****** in minimization

From: Thakur, Abhishek <axt651.miami.edu>
Date: Thu, 28 Jul 2016 18:37:42 +0000

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: 51135123.
>> 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
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