VMD-L Mailing List

From: Peter Freddolino (petefred_at_umich.edu)
Date: Sun Apr 15 2018 - 20:14:26 CDT

1. Please see my reply on namd-l.
2. Please don't rapidly cross post between vmd-l and namd-l

Thanks,
Peter

On Sun, Apr 15, 2018 at 7:57 PM, Rabeta Yeasmin <rabetayeasmin_at_gmail.com>
wrote:

> Dear VMD Users,
>
> I have converted an all-atom lipid-protein system to a coarse-grained
> system using residue based-coarse grained method (rbcg) where the protein
> was at the center of the lipid. Later I did Steered MD simulation and
> umbrella sampling simulation in the coarse-grained system. Now I want to
> convert the last structure from my simulation to all-atom structure
> (pdb file) where the protein is at 22A above the lipid. I was trying to do
> it in VMD using reverse-rbcg model. But after running a while, it just
> gets stuck. I had tried this several times and it has the same problem. I
> am not sure what can be the problem.
> Can you please suggest me what should I do?
>
> Thanks.
>