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

From: Rabeta Yeasmin (rabetayeasmin_at_gmail.com)
Date: Tue Sep 18 2018 - 10:58:25 CDT

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
>>
>
>

This archive was generated by hypermail 2.1.6 : Thu Sep 19 2019 - 23:19:58 CDT