Hi,
My system contains 20 amino acids around nanotube. I want to know the adsorption amount of AA DURING simulation time; the adsorption occurs when the distance between one of non-hydrogen atoms of AA and the tube surface was less than 0.5 nm. So how can i calculate this property? I use GROMACS and i have tried to do it g_dist tools but i couldn't reach a proper result. Any output!
Does anyone have experience on it?
(The adsorption number may not be integer because during simulation some AAs may absorb and reabsorb)
Best
Radial distribution function (RDF) can be useful for this purpose.
Dear Ramin Ekhteiari Salmas
Thank you, good idea!
I try it, but i'm a little confused in choosing best rdf tool's options,
g_rdf -f md2.xtc -s md2.tpr -surf mol -rdf mol_com
then i choose Nanotube as reference group and Protein-H as group1
Turning of normalization because of option -surf
Reading file md2.tpr, VERSION 4.5.4 (single precision)
Reading file md2.tpr, VERSION 4.5.4 (single precision)
Select a reference group and 1 group
Group 0 ( System) has 27843 elements
Group 1 ( Other) has 408 elements
Group 2 ( tube) has 408 elements
Group 3 ( Protein) has 690 elements
Group 4 ( Protein-H) has 360 elements
Group 5 ( C-alpha) has 30 elements
Group 6 ( Backbone) has 90 elements
Group 7 ( MainChain) has 90 elements
Group 8 ( MainChain+Cb) has 120 elements
Group 9 ( MainChain+H) has 180 elements
Group 10 ( SideChain) has 510 elements
Group 11 ( SideChain-H) has 270 elements
Group 12 ( Prot-Masses) has 690 elements
Group 13 ( non-Protein) has 27153 elements
Group 14 ( Water) has 26745 elements
Group 15 ( SOL) has 26745 elements
Group 16 ( non-Water) has 1098 elements
Select a group: 2
Selected 2: 'tube'
Select a group:
Selected 2: 'Protein-H'
I have attached the result. I think this shows most of Protein-H "ATOMS" are in about 0.5 nm far from nanotube, yes?
But that's not what i want. first, this tool should consider Z as a nanotube axis. then surface of nanotube (or at least Z axis of nanotube which pass center of mass point), then should consider each non-hydrogen atom of each AA representative of just 1 contact. I hope i'm clear. I want the NUMBER of contacts(here contact means 0.5 or
I’m not a gromacs user. But I’m sure there some tools in gromacs that can calculate RDF.
Gromacs has 'grdf' facility to calculate radial distribution function. Schrodinger's software suilte has an RDF panel that would do the same.
in my idea, Travis software is a good item for visualizing this analysis.
- Badges
- Science topic