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

From: Peter Freddolino (petefred_at_umich.edu)
Date: Mon Sep 17 2018 - 15:58:31 CDT

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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