Thanks, Bill!
Your protocol seems very useful.
1 Does it reasonable as well to use higher taup and taut constants during
equilibrating to prevent high fluctuations both in temperature and pressure?
2 Will the simulation in NVT be reasonable in case of membrane protein
simulation where membrane scaling are also very important for protein's
dynamics?
James
2014-06-21 3:57 GMT+02:00 Bill Ross <ross.cgl.ucsf.edu>:
> Ps - big pressure fluctuations are normal, search list for an explanation.
> I think my approach would work for any system, but I would see how previous
> papers on systems like yours have done it.
>
> -------- Original message --------
> From: James Starlight <jmsstarlight.gmail.com>
> Date:06/20/2014 11:31 AM (GMT-08:00)
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: Re: [AMBER] On the usage of the position restrains during
> equilibration
>
> Bill,
>
> many thanks for suggestion. But during amber workshop it has been mentioned
> that system should been heated in NVT initially. In this regards should
> the total workflow be
> 1) NVT (heating. system with applied posres on protein),
> 2) NPT (equilibration, system with applied posres on protein). <- what
> should be provided in input file for better stabilization of box volume?
> How much time water-soluble system should be equilibration? What outputs in
> log should be checked (I've always find big fluctuations in reassure with
> any barostat used) ?
> 3) NVT (production, free protein)- barostat turned off
>
> Will such approach (production in nvt instead of npt) be suitable for
> membrane protein simulation as well?
>
>
> James
>
>
> 2014-06-20 19:36 GMT+04:00 Bill Ross <ross.cgl.ucsf.edu>:
>
> > For what it's worth, I thought NVT is preferred for production and NPT to
> > equilibrate volume. Since NVT is faster and less artificial than scaling
> > the box to affect pressure.
> >
> > Bill
> >
> > -------- Original message --------
> > From: James Starlight <jmsstarlight.gmail.com>
> > Date:06/20/2014 7:30 AM (GMT-08:00)
> > To: AMBER Mailing List <amber.ambermd.org>
> > Subject: [AMBER] On the usage of the position restrains during
> > equilibration
> >
> > Dear Amber users!
> >
> > >From the Amber tutorials I've learn that initial heating should be
> always
> > done in NVT and production run in any desired ensemble. Supposing I'm
> > using NPT for production run performing 100ps NVT pre-equilibration of my
> > water-soluble system with applied position restrains on all atoms of my
> > protein. Should I do a short NPT equilibration as well (taking all
> outputs
> > from the previous NVT) with the such position restrains applied to the
> > protein (as I've found in the Gromacs tutorials). What fluctuation to the
> > system might be introduced by its initial coupling with the Monte Carlo
> > barostat (for instance seriously deforming protein conformations during
> > beginning of the NPT phase if pos.res on protein atoms have not been
> > applied) ?
> >
> >
> > TFH,
> >
> >
> > James
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Received on Fri Jun 20 2014 - 22:30:02 PDT
