Re: Bad structure after converting the coarse grained last frame to all-atom

From: Peter Freddolino (petefred_at_umich.edu)
Date: Tue Sep 18 2018 - 12:26:59 CDT

It looks like the do_rotations argument is set by default in the gui, but
just to confirm, could you try doing the reversal via the text interface
(see https://www.ks.uiuc.edu/Research/vmd/plugins/cgtools/) for
directions). Be sure to specify the value 1 for the do_rotations argument,
which should do its best to minimize the perturbations to the reversed
structure. Also, are you trying to reverse cg the water and ions? I would
not recommend doing so, but rather, reversing the lipid/protein and then
re-solvating.
Best,
Peter

On Tue, Sep 18, 2018 at 11:58 AM, Rabeta Yeasmin <rabetayeasmin_at_gmail.com>
wrote:

> Dear Mr. Peter,
>
> I have used CG Builder GUI in VMD to reverse the coarse-grained molecule.
> That did not ask me to set do_rotations argument. And my system contains
> two protein, POPC and POPG lipid, water and ions. I have used the RBCG
> model that is provided in VMD 1.9.2 as plugins. I think it is the old RBCG
> model from 2007.
>
> Thanks.
>
> Rabeta Yeasmin
>
> On Mon, Sep 17, 2018 at 3:58 PM Peter Freddolino <petefred_at_umich.edu>
> wrote:
>
>> Can you please clarify the precise command that you used to reverse
>> coarse grain the molecule? Did you have the do_rotations argument set? What
>> does your system contain?
>> Also, what CG model are you using? I would hope a recent martini version
>> and not the old RBCG model from 2007, unless you're trying to precisely
>> reproduce one of those old papers...
>> Best,
>> Peter
>>
>> On Mon, Sep 17, 2018 at 12:50 PM, Rabeta Yeasmin <rabetayeasmin_at_gmail.com
>> > wrote:
>>
>>> Dear NAMD users,
>>>
>>> I have run some coarse-grained simulation of a protein-lipid system in
>>> NAMD using residue-based coarse-grained simulation. After running 500ns, I
>>> have converted back the last structure of coarse-grained simulation to the
>>> all-atom system. But the structure has a lot of stretching. And during the
>>> minimization of the converted structure, it showed a lot f warning like-
>>> Warning: Tuple 540098 with atoms 20552(159) 20548(159) missing patch 129
>>>
>>> I have tried another way to overcome this kind of problem. I have
>>> minimized the last structure of coarse-grained simulation before
>>> converting it to the all-atom system. But that did not work too. Can you
>>> please suggest me what can cause this kind of problem?
>>> Thanks.
>>>
>>> Rabeta Yeasmin
>>>
>>
>>

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