[gmx-users] Re: change in secondary structure

Justin A. Lemkul jalemkul at vt.edu
Wed Feb 2 12:34:32 CET 2011

bharat gupta wrote:
> Hi,
> I think I have asked this question earlier in the forum .. that during 
> my 3ns simulation of a 230 amino acid proteins some portion of 2 beta 
> strands got converted to loop/random coil, after visualizing in VMD. I 
> checked the DSSP profile also .. and as per the DSSP results it's coil 
> in that region .. can anybody tell me where can the error be as I have 
> been checking my structure right from the minimization step till npt 
> equilibration and its was fine ... this has happened only after 
> simulation ... pls help ?? 

The comments I made last week still stand:


You're basing your conclusions on a 3-ns simulation, which I would say is far 
too short to obtain any meaningful data for such a system.


> -- 
> 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
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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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