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
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
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,
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