Re: [gmx-users] Gromacs Tutorial by Justin

On 3/10/18 1:24 PM, Faezeh Pousaneh wrote: Dear Justin One more question please, Do we need to have constraint in this model of CO2? Isn't it so that we have fixed the bond lengths and angles (180) in the topology by this method? The molecule behaves as a rigid rotor. The math is all laid

Re: [gmx-users] Gromacs Tutorial by Justin

Dear Justin One more question please, Do we need to have constraint in this model of CO2? Isn't it so that we have fixed the bond lengths and angles (180) in the topology by this method? I run 2 simulations, one with constraints = all-angles and the other with constraints = all-bonds, I get

Re: [gmx-users] Gromacs Tutorial by Justin

Thank you. Best regards On Wed, Mar 7, 2018 at 1:38 PM, Justin Lemkul wrote: > > > On 3/7/18 6:24 AM, Faezeh Pousaneh wrote: > >> Dear Justin, >> >> I have 2 questions regarding your tutorial on Carbon Dioxide in this link: >>

Re: [gmx-users] Gromacs Tutorial by Justin

On 3/7/18 6:24 AM, Faezeh Pousaneh wrote: Dear Justin, I have 2 questions regarding your tutorial on Carbon Dioxide in this link: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/vsites/index.html 1- I see that in your simple simulation you use no boundary conditions,

[gmx-users] Gromacs Tutorial by Justin

Dear Justin, I have 2 questions regarding your tutorial on Carbon Dioxide in this link: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/vsites/index.html 1- I see that in your simple simulation you use no boundary conditions, pbc=no, should it be always so for this model?