> > > > Message: 5 > Date: Tue, 19 Oct 2010 13:06:42 -0400 > From: "Justin A. Lemkul" <jalem...@vt.edu> > Subject: Re: [gmx-users] Re: Umbrella sampling with temperature and > pressure coupling method problem (Justin A. Lemkul) > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <4cbdd022.6020...@vt.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > > DeChang Li wrote: > > > > > > > > Message: 6 > > Date: Tue, 19 Oct 2010 09:30:47 -0400 > > From: "Justin A. Lemkul" <jalem...@vt.edu <mailto:jalem...@vt.edu>> > > Subject: Re: [gmx-users] Umbrella sampling with temperature and > > pressure coupling method problem > > To: Discussion list for GROMACS users <gmx-users@gromacs.org > > <mailto:gmx-users@gromacs.org>> > > Message-ID: <4cbd9d87.6080...@vt.edu <mailto:4cbd9d87.6080...@vt.edu > >> > > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > > > > > > chris.ne...@utoronto.ca <mailto:chris.ne...@utoronto.ca> wrote: > > > Use Langevin dynamics (the sd integrator) to control the > temperature. > > > You are sure to get the correct ensemble that way and if you are > > doing > > > US then you can not extract dynamics anyway. > > > > > > Hopefully somebody else can address the pressure coupling for > > you, but > > > probably you need to provide more information to get a useful > > answer there. > > > > > > > The Berendsen barostat suffers from the same limitations as the > > thermostat - the > > pressure distribution does not produce a true NPT ensemble. > > > > > > Whether the correct canonical ensemble (NPT or NVT) is important (or > > indispensable) for umbrella sampling? If I used the weak coupling method > > (Berendsen) to do the simulations, can I extract the PMF from the > > umbrella sampling simulations? > > > > I would think that a proper statistical mechanical ensemble would be > considered > indispensable for any simulation. In my mind, there is no real reason to > use > less accurate methods when collecting data. If your goal is a comparison > of > methods, or consistency with other results, sure, then you may have a > reason to > use algorithms that may be less than optimal. For any sensitive > thermodynamic > study, I would strongly argue that your potential energy surface needs to > be > rigorously correct. > > The point is this. You have to defend your choices to a skeptical audience > (reviewers). This is one question that might be asked, and really should > be. > Methods should be scrutinized. So I would ask you this: why perform your > simulations with algorithms that are not as accurate as others, when those > better algorithms are accessible to you and do not harm performance in any > demonstrable way? > > -Justin >
Thank you for your reply! So I will use Nose-Hoover for temperature coupling and Parrinello-Rahman for pressure coupling in the data collection. Anyway, I may do some simulations with Berendsen method to see if there is any difference in results when using the two coupling methods. > > > > > > > -Justin > > > > > -- original message -- > > > > > > Dear all, > > > > > > I want to use umbrella sampling to calculate the PMF of the > > > conformational transition of a protein. What temperature coupling > > method > > > and > > > pressure coupling method should I use? Berendsen temperature > > coupling or > > > Nose-Hoover temperature coupling? Or each one is OK? > > > > > > > > > > -- > > ======================================== > > > > Justin A. Lemkul > > Ph.D. Candidate > > ICTAS Doctoral Scholar > > MILES-IGERT Trainee > > Department of Biochemistry > > Virginia Tech > > Blacksburg, VA > > jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080 > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > > ======================================== > > > > > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > > >
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