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

From: Rabeta Yeasmin (rabetayeasmin_at_gmail.com)
Date: Tue Apr 17 2018 - 10:49:55 CDT

Hi Peter,

I have found the problem. Actually I was using a wrong reference all-atom
and psf file for reverting. I have tried with the correct one and it looks
better.
Thanks so much for your help.

Rabeta Yeasmin

On Mon, Apr 16, 2018 at 4:05 PM, Peter Freddolino <petefred_at_umich.edu>
wrote:

> 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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