Re: [gmx-users] on gmx make_ndx

2015-06-19 Thread Justin Lemkul 



On 6/18/15 8:13 AM, Brett wrote:

Dear Justin,


For the on-line command  g_dist -s run.tpr -f run.xtc -n index.ndx -o
dist.xvg, then for the ndx file, it should contain 2 group of atoms, for
example, 1 group is r 22  a OE2, the other group is r 137  a NH1. In the
single ndx file, should I name these 2 groups separately? Otherwise how does
g_dist determine the 2 groups for distance calculation? But if in the same
ndx file it include 3 groups, what g_dist will do?



The number of groups in the index file is irrelevant.  You will be prompted for 
two selections.  Choose whatever is relevant.  Hopefully you tried the command 
and got your answer in a few seconds rather than waiting all this time for my 
reply :)


-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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Re: [gmx-users] on gmx make_ndx

2015-06-18 Thread Justin Lemkul 



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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