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

From: Peter Freddolino (
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...

On Mon, Sep 17, 2018 at 12:50 PM, Rabeta Yeasmin <>

> 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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