[gmx-users] How to calculate which residues are within a certain distance from a carbon nanotube

[Justin Lemkul]

On 12/22/15 4:25 AM, soumadwip ghosh wrote:
> Hello,
>
>          I am simulating a single stranded DNA molecule in the presence of
> an armchair carbon nanotube using GROMACS 4.5.6. One of the reviewers of
> the paper has asked to calculate the numbers of nucleic acid bases are
> stacked to the CNT surface as a function of simulation time as well as
> which nucleobases are stacked to each other as a function of time
> similarly. I am planning to calculate the populations of bases as suggested
> by the reviewer withing a cut-off of 0.5 nm. Does anyone have any idea how
> to do it. As for example, g_dist -dist 0.5 option would give me the number
> of atoms not residue as a function of time. Can g_mindist in combination
> with -d 0.5 and -respertime serve the above purpose? Or should I try with
> g_select?
>

Use g_select.  g_dist and g_mindist will tell you about the number of atoms 
within a certain range.  You can use "same residue as" within g_select to get 
the actual number of residues that have atoms that satisfy your criteria.

-Justin

-- 
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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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