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

From: Peter Freddolino (petefred_at_umich.edu)
Date: Mon Apr 16 2018 - 16:05:39 CDT

That looks quite odd. But, are any of these crossing periodic cell
boundaries, either at the time that the system was coarse grained, or at
the time that you ran the reversal?
Thanks,
Peter

On Mon, Apr 16, 2018 at 12:07 PM, Rabeta Yeasmin <rabetayeasmin_at_gmail.com>
wrote:

> Hi,
> I have attached a image of my reverted all-atom system. The black one
> represents lipids and green and blue one are the two proteins. If you look
> closely, you will see that some of the black parts are not connected to the
> other parts and same with the two protein.
> Thanks.
>
> Rabeta
>
> On Mon, Apr 16, 2018 at 10:43 AM, Peter Freddolino <petefred_at_umich.edu>
> wrote:
>
>> 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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