Dear Justin, Thanks for your prompt reply! As you say, we should equilibrium each replica at its initial target temperature. So i guess we may do the followings: First, after the minimization and heating, we use NPT to equilibrium the density of the system. And then with the same initial system,equilibrium every replica at their target temperature with NVT ensemble to avoid the instability during REMD and keep the volume constant among the replicas. Finally, do the REMD simulations. Is this workflow reasonable enough and do you have any better guide? Any suggestions will be greatly appreciated! Best regards! Xiangqian Kong
--- On Mon, 11/14/11, Justin A. Lemkul <jalem...@vt.edu> wrote: > From: Justin A. Lemkul <jalem...@vt.edu> > Subject: Re: [gmx-users] The equilibrium before REMD simulations > To: "Discussion list for GROMACS users" <gmx-users@gromacs.org> > Date: Monday, November 14, 2011, 10:25 PM > > > ÏéÇ« ¿× wrote: > > Dear GMX users, I am puzzled about some technical > details regarding to the > > REMD simulation and eager for your generous help. With > the purpose to explore > > the additional conformational space of the protein, I > want to employ the REMD > > method in Gromacs. However, I noticed that in almost > all of the papers about > > REMD, a short equilibrium with NPT or NVT was > performed for each replica > > respectively before the final REMD run. But i think > the initial structure of > > each replica for REMD run is thus different due to the > respective equilibrium > > and may somewhat go against the concept of replicas > which i suppose should > > have same initial structures while with different > temperatures. So my > > question is whether we should or not perform the NVT > or NPT equilibrium > > before REMD simulations BTW and why? BTW, i also want > to know which ensemble > > Yes, always equilibrate. Otherwise, your systems will > almost certainly not be stable. Position restraints > are typically applied to the solute of interest during the > initial equilibration, making initial differences almost > insignificant. > > > should we use in REMD because some papers use NPT > while others use NVT. > > Pressure coupling algorithms frequently break down at high > temperature, so NVT is often used. > > -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 > > ======================================== > -- gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search > before posting! > Please don't post (un)subscribe requests to the list. Use > the www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
