Re: [gmx-users] elongated protein in production run

Hello Mark, Alright. However, building on previous .cpt I have extended my production run for 10 more ns. Thanks for you time. Much appreciated. On Thu, Apr 20, 2017 at 12:54 PM, Mark Abraham wrote: > Hi, > > This is entirely normal. Please see >

Re: [gmx-users] elongated protein in production run

Hi, This is entirely normal. Please see http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions Mark On Thu, Apr 20, 2017 at 9:16 AM abhisek Mondal wrote: > Hi, > > I'm trying to simulate a protein for 40ns after 20ns nvt and 20ns npt >

[gmx-users] elongated protein in production run

Hi, I'm trying to simulate a protein for 40ns after 20ns nvt and 20ns npt equilibration, respectively. After nvt and npt equilibration steps the protein looks fine to me. But when I analyze the trajectory file generated after 40ns of production run, I found some unusual facts. Half of the