VMD-L Mailing List

From: Rabeta Yeasmin (rabetayeasmin_at_gmail.com)
Date: Sun Apr 15 2018 - 18:57:10 CDT

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.