[gmx-users] Re: trjconv for pbc

2013-11-03 Thread rankinb
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

Re: [gmx-users] Re: trjconv for pbc

2013-11-03 Thread Justin Lemkul
On 11/3/13 7:12 AM, rankinb wrote: 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

[gmx-users] Re: trjconv for pbc

2013-11-02 Thread rankinb
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

Re: [gmx-users] Re: trjconv for pbc

2013-11-02 Thread Justin Lemkul
On 11/2/13 11:23 AM, rankinb wrote: 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

[gmx-users] Re: trjconv for pbc

2013-11-02 Thread rankinb
Here is a snapshot of what I was able to extract, if that helps. http://gromacs.5086.x6.nabble.com/file/n5012166/hs.png 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

2013-11-02 Thread rankinb
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

Re: [gmx-users] Re: trjconv for pbc

2013-11-02 Thread Justin Lemkul
On 11/2/13 12:25 PM, rankinb wrote: 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,