I have two groups defined in the index file. The group [ protein ] has all protein atoms and the group [ DNA_5 ] has all the atoms of residue id 5 of DNA. I want to calculate the distance between center of mass of [ DNA_5 ] and each residue of [ protein ]. These distance will be given w.r.t time, i.e., say there are 5 protein residues, I should get 5 distances (each residue-DNA_5 distance) for each snapshot.
Is it possible to do by gmx distance directly? If not please suggest me a possible script !!
The link may be useful
http://manual.gromacs.org/documentation/5.1/onlinehelp/gmx-distance.html
Thank you very much for the link. But I have tried all the possibilities but I cannot figure out the exact thing I need !!
You might also considering post-processing your trajectories in VMD to extract this data https://www.ks.uiuc.edu/Research/vmd/
Hi,
You have to specify all the residues of your proteins as separate groups in your index file and execute the gmx distance command prompting till your nth residue.
The command will be as follows:
gmx distance -f *.xtc -s *.tpr -select 'com of group "*protein_residue_number*" plus com of group "DNA_5"' -n *.ndx -oav output.xvg
Replace * with your specific file names. For *protein_residue_number* in the command, specify the group name for specific aminoacid. There has to be a single quotation at the start and end of the -select flag. Likewise for groups, there are double quotations at the start and end.
Thank you Syed. This is what I know. But say I have 100 residues in my protein, it may not be easy to make an index file with all the residues separately. hence, I was thinking is there is any other way !!!
Annemarie, Thank you. I guess writing a vmd-tcl script would be better in this case.
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