[gmx-users] conformational change

Julio Dominguez acheron24 at hotmail.com
Fri Dec 14 14:57:00 CET 2012

Morning Shine and Tsjerk, 
Sorry for the missing links (here and here), I was refering to PyMol wiki's and a blog:
But what Tsjerk mentions is far more relevant, I was thinking statically last night. First off, PyMol automatic secondary structure detection is spotty. Second, the command dss within PyMol does a better job. Third, the most systematic way to visualize secondary structure  within Pymol would be to use DSSP (or Stride) within PyMol.
Thinking dynamically, you could run do_dssp, part of Gromacs, and check the time course of the whole secondary structure during your simulation. There is also g_helix, which can output the % of time a structure spends as a helix.
As everybody has pointed out, the forcefield is the most probable cause. Be sure to check recent literature to make sure the ff you are using is not biased against (or in favor) of helical structures.
Best regards.
> Message: 4
> Date: Fri, 14 Dec 2012 09:50:28 +0100
> From: Tsjerk Wassenaar <tsjerkw at gmail.com>
> Subject: Re: [gmx-users] conformational change
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
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> Hey Julio, Shine,
> I would like to see the 'here' and 'here'. Pymol has two routines for
> determining secondary structure, one of which uses the same approach as
> dssp to classify helices and sheets. A relevant question is, what is a
> helix? Is a helix a stretch of residues that is defined by dssp as helix?
> That is also just a heuristic.
> Justin is quite right that what is observed is largely the consequence of
> the force field and settings. Make sure that the force field and settings
> you use reproduce proper behaviour. The structure will not just change
> because of the placement of waters, or that shouldn't be a persistent
> effect.
> And why would it be a helix for all of the residues for all of the time?
> Because the crystal structure shows it's a helix? Maybe it's more flexible
> in solution and only a helix for a given proportion of time. If you're
> afraid to see (temporary) loss of structure, then it may be better not to
> simulate at all.


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