[gmx-users] on gmx make_ndx

[Brett]

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?


Brett


 





At 2015-06-18 19:32:58, "Justin Lemkul" <jalemkul at vt.edu> wrote:
>
>
>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
>
>jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>http://mackerell.umaryland.edu/~jalemkul
>
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