[gmx-users] change in secondary structure after npt equilibration

Justin A. Lemkul jalemkul at vt.edu
Fri Jan 28 13:23:22 CET 2011

bharat gupta wrote:
> Hi,
> I am doing a simulation of a 230 amino acid protein for 3ns ... and I 
> have completed the npt equilibration step .. After retrieving the 
> structure from npt step and viewing it in pymol, reveals that some 
> portion of the beta strand got changed to a loop but when I visualized 
> the same structure in VMD I found that nothing has happened to the 
> structure .. In order to confirm more ... I generated the SS profile 
> using dssp and I found that , the dssp shows E i.e. sheet for that 
> region .. So what shall i do next ... shall I continue with the 
> production step or not ??

Visualization programs are not always reliable in what they show you, we've 
discussed that.  Methods like DSSP and STRIDE are far more trustworthy, and seem 
to indicate that your structure is fine.  What you should be much more concerned 
with at this point is whether or not your equilibration sufficiently converged 
all of the thermodynamic observables.


> -- 
> Bharat
> Ph.D. Candidate
> Room No. : 7202A, 2nd Floor
> Biomolecular Engineering Laboratory
> Division of Chemical Engineering and Polymer Science
> Pusan National University
> Busan -609735
> South Korea
> Lab phone no. - +82-51-510-3680, +82-51-583-8343
> Mobile no. - 010-5818-3680
> E-mail : monu46010 at yahoo.com <mailto:monu46010 at yahoo.com>


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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