Open ErikPoppleton opened 10 months ago
I actually cannot reproduce this issue, since the latest oxDNA version and the one compiled from here give me very similar energies and similiar stretched configurations such as this one:
Erik, any news on this one?
Describe the bug When pulling structures into desired starting configurations using mutual traps, the version of oxDNA running on the
oxServe
plugin of oxView is significantly more stable than the current version here (or this fork by @Jonahowns). I have not been able to successfully compile the old version used by oxServe for local testing (which is using code from this repository. I don't know the specific checkout, maybe @zoombya can double check?). This implies that one or more of the following is different between this older version of oxDNA and the current (post move to GitHub) implementations:To Reproduce pull_test.zip The attached zip file contains a simulation where this behavior occurs. This structure is stable with the default oxServe input file, but the very similar input file in the example will explode within the first 10000 steps if run on the current oxDNA. The structure can be made stable by decreasing the
dt
10x and themax_backbone_force
100x.Expected behavior It would be nice to know what changed between the two versions. It would also be nice if the older oxDNA_anm version of relaxation turns out to be physically reasonable and the current behavior could be updated to match because it is much more successful at producing starting structures for simulations.
Desktop (please complete the following information):