[gmx-users] Trajectories

I am interested in pulling out the trajectories (x,y,z coordinates) of water molecules within a certain distance of my solute molecule. I have tried using g_select, but that will only give me the atom numbers and not the trajectories. I can create an index file using this command but unfortunatel

[gmx-users] XYZ Cordinates of a subsset of atoms

Is there a way to create a .gro file with the XYZ coordinates of atoms that are within a specified distance of another atom at each time frame? It seems that trjconv should be able to do this but I am having a difficult time figuring it out. Thank you, Blake -- View this message in context:

[gmx-users] trjconv for pbc

Hi all, I am trying to use trjconv to remove PBC. More specifically, I would like to extract the coordinates of all the water molecules within a certain distance of a single solute molecule. However, I have been unsuccessful in doing so, even after following the guidelines on the GROMACS website

[gmx-users] Re: trjconv for pbc

Tsjerk, Thanks for your reply. I have tried using the center option, but ran into similar problems. Here are the exact commands that I used: g_select -f file.xtc -s file.tpr -n index.ndx -select 'group 14 and within 0.71 of group 13' -b 37.875 -e 37.875 -on index1 (where group 14 contains the w

[gmx-users] Re: trjconv for pbc

Here is a snapshot of what I was able to extract, if that helps. Blake PhD candidate Purdue University Ben-Amotz Lab -- View this message in context: http://gromacs.5086.x6.nabble.com/trjconv-for-pbc-tp5012160p5012166.html Sent from the

[gmx-users] Re: trjconv for pbc

Here are the steps that I used: 1. trjconv -pbc whole -dump 37.875 2. trjconv -pbc nojump 3. trjconv -center 4. g_select to make an index containing the atoms of interest 5. trjconv to extract coordinates Regardless of whether step 1 is used or not, the resulting coordination shell configura

[gmx-users] Re: trjconv for pbc

That last procedure works. I really appreciate your help. The only other question I have is related to the selection process. Is there a way to select the oxygen atoms of water within a certain distance of a molecule, as well as the corresponding hydrogen atoms on the water molecule? Right now,

[gmx-users] Number of water molecules around any methyl carbon

Hi all, I would like to calculate the number of water molecules around any of the methyl carbon atoms of tert-butyl alcohol. Currently, I have defined an index group containing all three of the methyl carbon atoms and used trjorder -nshell to calculate the number of oxygen atoms within a specifi