[gmx-users] Still having issues analyzing normal-mode hessian

l-mode specific programs so I don't know how to begin troubleshooting. Thanks, *Bryan Roessler | Graduate Research Assistant* UAB | The University of Alabama at Birmingham *uab.edu/cmdb* Knowledge that will change your world -- gmx-users mailing listgmx-users@gromacs.org http://list

Re: [gmx-users] Normal Mode Analysis -- Expected Output

oel wrote: > On 2013-04-11 17:57, Bryan Roessler wrote: > >> Hello, >> >> I am running a normal mode analysis on a ~1500AA protein with the >> following >> mdp parameters: >> >> Log file opened on Tue Apr 9 09:55:00 2013 >> Host: uv1 pid: 1289

[gmx-users] Re:

Thank you for your response. I am running double precision gromacs and I have minimized my structure down to ~1 Fmax, so neither of those concerns should be a problem. On Thu, Apr 11, 2013 at 12:15 PM, abhijit Kayal wrote: > > in normal mode analysis you will get 3n vibrational degrees of freedo

[gmx-users] Normal Mode Analysis -- Expected Output

Hello, I am running a normal mode analysis on a ~1500AA protein with the following mdp parameters: Log file opened on Tue Apr 9 09:55:00 2013 Host: uv1 pid: 128985 nodeid: 0 nnodes: 64 Gromacs version:VERSION 4.6.1 Precision: double Memory model: 64 bit MPI library:

[gmx-users] ATP all-atom FF in GROMACS (CHARMM36?)

ould use some help in understanding how to convert toppar stream entries from CHARMM into the GROMACS format. Thank you, Bryan Roessler The University of Alabama-Birmingham -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search th