Re: [gmx-users] tpbconv subset

2010-05-24 Thread Justin A. Lemkul
John Shultz wrote: I modified the .mdp file, created a full system tpr, then ran it through tpbconv, then ran mdrun using the original xtc. It says the atom numbers don't match. mdrun -rerun md.xtc -v -s lig.tpr --- Program mdrun, VERSION 4.

Re: [gmx-users] tpbconv subset

2010-05-24 Thread John Shultz
I modified the .mdp file, created a full system tpr, then ran it through tpbconv, then ran mdrun using the original xtc. It says the atom numbers don't match. mdrun -rerun md.xtc -v -s lig.tpr --- Program mdrun, VERSION 4.0.5 Source code file: m

Re: [gmx-users] tpbconv subset

2010-05-23 Thread Justin A. Lemkul
John Shultz wrote: Justin, Only problem is I need to change this parameter energygrps to track the energy on specific groups in the simulation. Is there a way to modify the simulation parameters to track these energies? Modify the .mdp file the way you need to, create a full-system .tpr fi

Re: [gmx-users] tpbconv subset

2010-05-23 Thread John Shultz
Justin, Only problem is I need to change this parameter energygrps to track the energy on specific groups in the simulation. Is there a way to modify the simulation parameters to track these energies? On Sun, May 23, 2010 at 5:07 PM, Justin A. Lemkul wrote: > > > John Shultz wrote: >> >> I want

Re: [gmx-users] tpbconv subset

2010-05-23 Thread Justin A. Lemkul
John Shultz wrote: I want to run a subset of an original trajectory. I know how to get the tpr consisting of the subset. How do I modify the simulation with a new mdp file and then run the mdrun? I was referencing these instructions If you have a .tpr file, then the .mdp file is a step backw