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

soumadwip ghosh soumadwipghosh at gmail.com
Tue Dec 22 10:25:28 CET 2015


        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

Sorry if I am asking for much.

Thanks and regards,
Soumadwip Ghosh
Research Fellow

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