Re: [AMBER] Constant pH simulation in explicit solvent

From: Nikolay N. Kuzmich <nnkuzmich.gmail.com>
Date: Thu, 2 Aug 2018 13:32:35 +0300

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Hello Eric,

thank you for your advice!

Kind regards,
Nick


------------------------------

Message: 4
Date: Wed, 1 Aug 2018 10:19:53 +0000
From: Eric Lang <eric.lang.bristol.ac.uk>
Subject: Re: [AMBER] Constant pH simulation in explicit solvent
To: AMBER Mailing List <amber.ambermd.org>
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Dear Nick,


It is better to switch on CpHMD *after* the NPT equilibration.


See this thread: http://archive.ambermd.org/201611/0189.html

In particular Jason's reply:

'- Is it possible to run CpHMD (not pH-REMD) in NPT?


Yes, but you run the risk that

the fluctuating charge can throw off the
density due to finite size effects (the pressure and free energy is
sensitive to net charges when using the net neutralizing plasma like Amber
 does.'



On another note, the parametrisation of the reference compounds has been
done with TIP3P.

I do not know if other water models have been tested and if they have an
effect.

It is probably better to use TIP3P unless this is fully tested.


Hope this helps,


Eric 


--
Eric Lang
BrisSynBio Postdoctoral Research Associate Modelling
Centre for Computational Chemistry
School of Chemistry - University of Bristol
Bristol BS8 1TS - United Kingdom
2018-08-01 12:32 GMT+03:00 Nikolay N. Kuzmich <nnkuzmich.gmail.com>:
> Dear Amber users,
>
> I would like to make clear how a constant pH simulation in explicit solvent
> is performed:
> 1. ASP, GLU and HIS are renamed into AS4, GL4 and HIP in the pdb file.
> 2. tleap is opened, leaprc.constph and the pdb are loaded off.
> 3. The system is neutralized/necessary ions are added and solvated (SPC/E,
> OPC, etc).
> 4. prmtop and inpcrd file are saved.
> 5. prmtop file with the new radii is obtained employing cpinutil.py
> 6. The system is minimized and heated (PBC).
> 7. The system is equilibrated (NPT) and the production run is started.
> Is icnstph=2 option introduced with the beginning of NPT equilibration or
> at which stage?
>
> Thank you in advance,
> Nick
>
> Nikolay Kuzmich
> Department of Drug Safety,
> Research Institute of Influenza,
> WHO National Influenza Centre of Russia,
> 15/17 Professor Popov St.,
> Saint-Petersburg
>
>
>
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Received on Thu Aug 02 2018 - 04:00:02 PDT
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