[gmx-users] Distance-force relationship on pulling
Pablo Galaz Dávison
Pabloglald at hotmail.com
Thu Feb 2 00:10:07 CET 2017
Dear Gromacs users,
I am performing several steered molecular dynamics simulations and I would like to analyze my force-extension curves using the protein's end to end distance. I am pulling by fixating all atoms in the first residue, and pulling all the atoms in the last one for a protein.
So far I have calculated the protein displacement by calculating total distance as =time*pulling rate, and substracting the "spring" length as = - total distance / spring constant.
Nevertheless, when I compare this FEC to one obtained using VMD's end-to-end distance they are very similar, yet the latter is always less stretched (about less than 10 angstrom).
So my question: is there any reason for which it may be incorrect to calculate protein's displacement by substracting the "spring"? or is it just my vmd measurements that are not right?
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