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

From: Rabeta Yeasmin (rabetayeasmin_at_gmail.com)
Date: Mon Apr 16 2018 - 10:41:11 CDT

Hi, Peter,

Thanks. It worked without reverting water. But It looks like some parts of
lipid and protein are detached from other parts. I am not sure if it is
usual during reverting to all-atom.

Rabeta Yeasmin

On Sun, Apr 15, 2018 at 7:57 PM, Peter Freddolino <petefred_at_umich.edu>
wrote:

> 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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