[gmx-users] Distance-force relationship on pulling

[Pablo Galaz Dávison]

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?


Thank you

Pablo Galaz