Re: [gmx-users] Umbrella sampling on lipid bilayer

2019-09-30 Thread John Whittaker
> Dear gromacs users, > > Sorry for repeating my question. > > I didn't receive any email so I couldn't reply and I missed > > them. Hi, Justin replied in this mail: https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2019-September/126735.html Best, John > > I am using following

Re: [gmx-users] Umbrella sampling on lipid bilayer

2019-09-25 Thread Justin Lemkul
On 9/25/19 5:50 AM, Mahsa Rezaei wrote: Dear Dr. Warren Thanks for your response . I made my protein-membrane system with charmm-gui. so my force is charmm36. I used the equilibration input files that charmm-gui provide , and run 400 ns simulation for equilibration of my system . RMSD ,

Re: [gmx-users] Umbrella sampling on lipid bilayer

2019-09-25 Thread Mahsa Rezaei
Dear Dr. Warren Unfortunately,I missed your reply! Thanks for your response . I made my protein-membrane system with charmm-gui. so my force is charmm36. I used the equilibration input files that charmm-gui provide , and run 400 ns simulation for equilibration of my system . RMSD ,

Re: [gmx-users] Umbrella sampling on lipid bilayer

2019-09-24 Thread Dallas Warren
Does it do that without using the pull code, i.e. just performing NPT simulation? What is physically happening? Sounds like the bilayer is unstable. What forcefield is this? Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash