Re: [gmx-users] Extracting the timestep value from topology and/or trajectory files

On 2/21/13 9:47 AM, shavit wrote: Hello, For several months now, I've been writing my own analysis tools using the GROMACS template.c file. There is one thing I haven't been able to figure out, and that is how to get the timestep size. I'm confident this parameter is located in either the

Re: [gmx-users] Distance for window spacing in US?

So in umbrella sampling, does it really matter if the vector connecting the COMs of protein and ligand is NOT parallel with the vector of the pulling force (although the pull rate is 0)? I guess as long as the force in each sampling window is along the same direction, we can in theory get

Re: [gmx-users] Statistical uncertainty in gromacs

Hi Matthew, Thanks for your reply. I tried g_analyze as you suggested: 1) I am wondering why the average given by g_energy and g_analyze are not identical. I tried the following: g_energy -f Potential. edr -o Potential.xvg and extracted the average then provided Potential.xvg as input to

Re: [gmx-users] Statistical uncertainty in gromacs

On 2/21/13 6:58 PM, Juliette N. wrote: Hi Matthew, Thanks for your reply. I tried g_analyze as you suggested: 1) I am wondering why the average given by g_energy and g_analyze are not identical. I tried the following: g_energy -f Potential. edr -o Potential.xvg and extracted the average

[gmx-users] order in index and matrix

Dear users, I just wanted a small clarification whether the order of elements in matrix (-hbm) corresponds to reverse order of elements in the index file (-hbn) obtained from g_hbond? Thank you Kavya -- gmx-users mailing listgmx-users@gromacs.org