[gmx-users] Re: change in secondary structure

[Justin A. Lemkul]

bharat gupta wrote:
> Thanks for ur kind reply Justin ...
> 
> I also searched the gmx userlist regarding the same query and I found 
> out that It was mentioned to repeat the simulation again with a 
> different force field .. but I don't know about the energy minimization 
> parameters as  I am following ur lysozyme tutorial  for that .. I will 
> get back to u get if I get the same type of structural changes with this 
> force field... 
> 
> Also I would like to mention one more thing .. as I did the simulation 
> of crystal str of GFP with the same parameters which I used for the 
> variant of GFP .. In case of the crystal str. simulation result, it 
> seems to be perfectly fine and there is no change in the secondary 
> structure also ... So, if I am not wrong then there is some problem with 
> the variant structure that I have modeled ??.. Actually the variant of 
> GFP that I have modeled has one loop (of 4 amino acid in original str) 
> replaced with an another loop of 9 residues length ... CAn this be the 
> reason ??
> 

You cannot draw any sort of reliable conclusions from a single trajectory of 
such short length.

> Regarding the simulation time I want to ask ... what is the minimum or 
> the optimal time the structure should be simulated for such analysis as 
> I have read many paper published in big journals doing simulation only 
> for 1ns (in that case I am doing for 3 ns)... pls comment
> 

There is no hard and fast rule for how long an MD simulation needs to be.  You 
need to collect sufficient data over a sufficient time period to model the 
behavior of interest, with the understanding of how long it should take for that 
certain phenomenon to occur.  Expectations also scale with the quality of the 
software and hardware.  The paper you linked before was from 1999, at which time 
the expectations of simulation length were exponentially shorter.  Most systems 
aren't even completely stable after only 1 ns of unrestrained MD.  Nowadays, 1 
ns can be completed in a matter of hours, so the expectation (by reviewers and 
journals) is that far more data can be collected such that you approach a 
biologically-relevant time scale.

For loop movement, 3 ns is at least 10 times too short, in my experience.  50 or 
100 ns would be more appropriate, but don't just take my word for it.  You 
should also conduct independent simulations (i.e., different starting velocities 
applied to the same structure) to run multiple simulations and do proper 
statistical analysis.  You wouldn't do one single assay at the bench, so why 
would you do one single simulation and expect it to be absolutely correct?  It 
is possible that a single simulation shows erroneous behavior and can be 
eliminated as an outlier with sufficient replicates and data analysis.

-Justin

> On Wed, Feb 2, 2011 at 3:34 AM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     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:
> 
>     http://lists.gromacs.org/pipermail/gmx-users/2011-January/058014.html
> 
>     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.
> 
>     -Justin
> 
>         -- 
>         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>
>         <mailto:monu46010 at yahoo.com <mailto:monu46010 at yahoo.com>>
> 
> 
>     -- 
>     ========================================
> 
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
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> 
> 
> -- 
> 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
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================