It seems difficult to implement PBC with custom restraints for me, because I can't even don't know which default constraints need to be modified.
About the crashes, previously I ran on Ubuntu 18.04, it failed for segmentation fault. Today I updated my Linux to 22.04, and now it won't crash, but a max_molpdf issue arises.
Anyway, thank you so much for your reply!
Best regards! Qizan Chen
On Wed, Apr 3, 2024 at 5:09 PM Modeller Caretaker modeller-care@salilab.org wrote:
> On 4/3/24 12: 56 PM, Qizan Chen via modeller_usage wrote: > Can the > Modeller take periodic boundary conditions into account > during modeling? > No, Modeller has no built-in support for periodic boundary conditions. You > can add custom restraints > ZjQcmQRYFpfptBannerStart > This Message Is From an External Sender > This message came from outside your organization. > > ZjQcmQRYFpfptBannerEnd > > On 4/3/24 12:56 PM, Qizan Chen via modeller_usage wrote: > > Can the Modeller take periodic boundary conditions into account > > during modeling? > > No, Modeller has no built-in support for periodic boundary conditions. > > You can add custom restraints to the scoring function (see, e.g.https://urldefense.com/v3/__https://salilab.org/modeller/10.5/manual/node480...) so in principle > you could replace the existing restraints with PBC-aware versions, e.g. > rather than calculating the distance between A and B, return the > distance between A and the nearest image of B. However, this would be a > significant undertaking. > > > I noticed that symmetry constraints can be added > > They can, but Modeller's symmetry restraints would likely not be very > efficient here, since they don't remove any degrees of freedom. > > > but my original system is already large, and adding additional images > > causes crashes. > > Modeller should not crash with any size system, unless you run out of > physical memory, so I'm curious to know what your problem is here. > > Ben Webb, Modeller Caretaker > -- modeller-care@salilab.org https://urldefense.com/v3/__https://salilab.org/modeller/__;!!KwNVnqRv!FEsVB... > Modeller mail list: https://urldefense.com/v3/__https://salilab.org/mailman/listinfo/modeller_us... > >