Re: Reverting coarse-grain system to all-atom system

From: Peter Freddolino (petefred_at_umich.edu)
Date: Sun Apr 15 2018 - 19:57:33 CDT

1. If you're trying to reverse cg water, don't. Just re-solvate the system
after the converison.
2. If that doesn't help, give us an idea of what the console output looks
like and whether it still seems to be working. The cg reversal should be
pretty verbose...

Best,
Peter

On Sun, Apr 15, 2018 at 7:49 PM, Rabeta Yeasmin <rabetayeasmin_at_gmail.com>
wrote:

> Dear NAMD 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.
> Rabeta Yeasmin
>

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