Re: Bonds are too long after simulation

From: flavio seixas (
Date: Wed Sep 07 2011 - 13:10:13 CDT

Hy Tony,

If you want to get the bonds, angles and planarity close to ideal values, you must minimize your structure at the end of simulation.


--- On Wed, 9/7/11, Anthony Rey <> wrote:

> From: Anthony Rey <>
> Subject: namd-l: Bonds are too long after simulation
> To:
> Date: Wednesday, September 7, 2011, 4:32 PM
> Hi,
> Thanks for accepting my email address on the mailing list.
> I have been using NAMD for a while now but can't figure out
> what's going on with the simulation.
> I am basically doing the same simulation as the Ubiquitin
> unfolding tutorial except I use it for a protein structure
> that I solved by NMR.
> I created the psf from the pdb and made sure that I didn't
> get any error messages (except from the N-terminal and
> C-terminal residues : poorly guessed residues).
> Then, I ran a script to put my protein into a water sphere.
> The output files look normal (both psf and pdb). I ran the
> simulation (5000 minimisation steps + 50 000 steps for the
> simulation), put the right diameter and center of the sphere
> for the spherical boundary conditions into the configuration
> file.
> When I look at the output, the minimization was long enough
> and the system looks quite stable at the end of the
> simulation. However, I do get some abnormalities when I look
> at the structure into VMD: the bonds get bigger during the
> simulation.
> The bonds are bigger but they are not huge. From what I've
> seen in the forum, a lot of people have similar issues
> except that they got huge bonds which I don't. I don't have
> long bonds at the beginning of the simulation, and I don't
> have any atoms that have {0.00 0.00 0.00} coordinates in the
> pdb either. The bonds just increase in length during the
> experiment, and the longer the experiment, the longer the
> bonds....
> Is is normal that the bond length increases with the
> simulation? Is there a way to fix this?
> I would really appreciate your help as I have no idea how
> to fix this. Please let me know if you need further details
> about the simulation.
> Best regards,
> Tony

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