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, the resulting coordination
shell configuration is not complete in the sense that it looks like the
figure I posted previously. In all steps, I used the same .tpr file...is it
possible that I need to generate a new one after step 1?
1. trjconv -center -pbc mol -dump 37.875
As long as you're choosing an appropriate index group here (i.e., the single
solute molecule of interest), you should not need any further invocations of
trjconv before extracting coordinates. Pop open the resulting coordinate file
in your favorite visualization software and verify. It should be very obvious
if it worked as expected.
2. Make selection
3. Extract
-Justin
--
==================================================
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
==================================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
