[gmx-users] NPT-REMD

Hi All, I have been trying to perform NPT-REMD with a Protein Substrate and water. I am trying to use md+nose-hoover thermostat and parrinello-rahman barostat. However, I am not quite sure about the tau-t and the tau-p that I should be using here. I paste a part of my mdp file below: define

Re: [gmx-users] Re: NPT-REMD

Sorry. Yes. I meant different replicas have different average pressures. Thanks for the suggestions. On Sun, Aug 25, 2013 at 9:06 PM, Michael Shirts wrote: > Can you clarify - Do you mean that different replicas have different > average pressures? > > WITHIN each replica, the +/- 2000 bar chang

[gmx-users] Regarding Position restraint and freezegroups

Hello, I have been performing simulations with nanotubes. I read several entries in the gromacs users forum regarding the correctness of the usage of the freeze groups in simulations. However, I am trying to perform NPT simulations at two different temperatures using berendsen and parrinello-rahma

Re: [gmx-users] Regarding Position restraint and freezegroups

4:59 PM, Justin Lemkul wrote: > > > On 8/29/13 3:25 PM, rahul seth wrote: > >> Hello, >> >> I have been performing simulations with nanotubes. I read several entries >> in the gromacs users forum regarding the correctness of the usage of the >> freeze grou

Re: [gmx-users] Constraining a part of the system

Thanks On Tue, Sep 17, 2013 at 10:03 AM, Justin Lemkul wrote: > > > On 9/17/13 10:00 AM, HANNIBAL LECTER wrote: > >> Is there a way to constraint bonds of a part of the system while keeping >> the other part flexible? For example for a simulation with two proteins, I >> would like to constraint