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

From: Peter Freddolino (petefred_at_umich.edu)
Date: Mon Apr 16 2018 - 10:43:49 CDT

Hi Rabeta,
Could you be more specific? Images or actual coordinate files would be
useful.
Thanks,
Peter

On Mon, Apr 16, 2018 at 11:41 AM, Rabeta Yeasmin <rabetayeasmin_at_gmail.com>
wrote:

> 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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