On 6/18/15 1:08 AM, Brett wrote:
Dear All,
In http://www.gromacs.org/@api/deki/files/198/=gmx-tutorial.pdf, there is
make_ndx -f run.gro
At the prompt, create a group for GLU22 with “r 22”, ARG137 with “r 137”, and
then
“q” to save an index file as index.ndx. The distance and number of hydrogen
bonds
can now be calculated with the commands
g_dist -s run.tpr -f run.xtc -n index.ndx -o dist.xvg
Here for g_dist, it is the distance between GLU22 and ARG137, does it mean the
distance between the center of GLU22 and the cnter of ARG137? If so how does
GROMACS determine the center of a residue? If I want to get the distance
between one specific atom of GLU22 (for example OE2) and one specific atom of
ARG137 (for example NH1), how do I specify the residue and the atom of the
residue together in the make_ndx ?
g_dist calculates center-of-mass distances.
Making index groups of single atoms is easy in text editor (just write the atom
number you want) or with make_ndx syntax (type 'help' at the prompt to see
examples), e.g.
r 22 & a OE2
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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