Re: [gmx-users] Regarding TCoupling and position restraints

On 8/17/13 12:10 AM, HANNIBAL LECTER wrote: Thanks. Is there any way to position restraint a part of the system while keeping all bonds flexible? Sure. Apply position restraints as normal and set "constraints = none" in the .mdp file. This will affect your choice of dt, though, and SETTLE

Re: [gmx-users] Regarding TCoupling and position restraints

Thanks. Is there any way to position restraint a part of the system while keeping all bonds flexible? On Fri, Aug 16, 2013 at 5:24 PM, Justin Lemkul wrote: > > > On 8/16/13 5:09 PM, HANNIBAL LECTER wrote: > >> Hi, >> I am trying to simulate nanotube (1156) with protein and water and I am >> usi

Re: [gmx-users] Regarding TCoupling and position restraints

On 8/16/13 5:09 PM, HANNIBAL LECTER wrote: Hi, I am trying to simulate nanotube (1156) with protein and water and I am using Tcoupl = system using sd integrator in gromacs. Since I am position restraining the nanotube, I would expect that the restrained CNT degrees of freedom are accounted for

[gmx-users] Regarding TCoupling and position restraints

Hi, I am trying to simulate nanotube (1156) with protein and water and I am using Tcoupl = system using sd integrator in gromacs. Since I am position restraining the nanotube, I would expect that the restrained CNT degrees of freedom are accounted for while calculating the system temperatures usin