VMD-L Mailing List

From: Ryan McGreevy (ryanmcgreevy_at_ks.uiuc.edu)
Date: Thu Oct 06 2016 - 15:08:44 CDT

It's possible the density-derived forces are too high. You can try lowering
your gridforcescale until the system is more converged. Also make sure you
are using the appropriate restraints (secondary structure, chirality,
cispeptide).

On Thu, Oct 6, 2016 at 2:53 PM Steven Cohen <secohen_at_mit.edu> wrote:

> I'm running MDFF to fit a .pdb into my EM density map and have noticed
> that my simulations are running to near (~90%) convergence before cutting
> out due to exceeding the per-atom velocity. To the best of my knowledge,
> this seems to occur as the structure is getting pulled into the core of the
> EM density. Is there a good way to stop the program from cutting out so
> that I can reach a final structure?
>
> --
> Steven Cohen
> Graduate Student, Drennan Lab
> Department of Chemistry
> Massachusetts Institute of Technology
> secohen_at_mit.edu
>