Re: [gmx-users] Which .tpr file to use for g_rms?

On 4/12/2010 6:45 PM, Anirban Ghosh wrote: Thanks a lot for the reply. But I am getting different results with the two .tpr files (first and last) using the following commands: trjconv -s *first.tpr *-f test.xtc -o str.gro -dump 1 -pbc nojump trjconv -s *last.tpr* -f test.xtc -o str.gro

Re: [gmx-users] Which .tpr file to use for g_rms?

Anirban Ghosh wrote: Hi ALL, Its a very basic question but still... When we calculate RMSD (or any other parameter) using the g_rms command, we need to supply the .tpr file with -s option. Now suppose if I have a total 20 ns simulation with 4 breaks (i.e 5 ns in each run), then there will

Re: [gmx-users] Which .tpr file to use for g_rms?

Thanks a lot Justin for the reply. Yes, I understand that. But ideally which structure should be used as the reference, in a general, the starting structure or the end structure? like when I an using trjconv to dump my last frame (with -pbc nojump), which .tpr file should I use to get the exact

Re: [gmx-users] Which .tpr file to use for g_rms?

Anirban Ghosh wrote: Thanks a lot Justin for the reply. Yes, I understand that. But ideally which structure should be used as the reference, in a general, the starting structure or the end structure? That's up to you to decide based on what you need to measure. Do you want the RMSD

Re: [gmx-users] Which .tpr file to use for g_rms?

Thanks a lot for the reply. Actually I am running a protein in lipid bilayer. Now I want to calculate the thickness of the bilayer at the end of the simulation. So for that I want the last structure (.gro) file. So I am trying to dump the last structure using trjconv (with -pbc option). So to do

Re: [gmx-users] Which .tpr file to use for g_rms?

On 4/12/2010 4:33 PM, Anirban Ghosh wrote: Thanks a lot for the reply. Actually I am running a protein in lipid bilayer. Now I want to calculate the thickness of the bilayer at the end of the simulation. So for that I want the last structure (.gro) file. So I am trying to dump the last structure

Re: [gmx-users] Which .tpr file to use for g_rms?

Thanks a lot for the reply. But I am getting different results with the two .tpr files (first and last) using the following commands: trjconv -s *first.tpr *-f test.xtc -o str.gro -dump 1 -pbc nojump trjconv -s *last.tpr* -f test.xtc -o str.gro -dump 1 -pbc nojump So which .tpr file