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 index1 (where group 14 contains
the water molecules and group 13 is the solute molecule)
trjconv -s file.tpr -n index1.ndx -f file.xtc -o out.gro -b 37.875 -e 37.875
trjconv -f out.gro -s file.tpr -n index.ndx -o out2.gro -center
Does this procedure seem reasonable?
Right commands, wrong order.
1. Center on the solute
2. Make selection
3. Extract coordinates
Note that specifying -b and -e with the same time can fail in some cases; use
-dump instead.
-Justin
--
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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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