[gmx-users] Change in structure after solvation_Gromacs

[Justin A. Lemkul]

ms wrote:
> On 05/12/10 10:39, swagata chakraborty wrote:
>> I was trying to run MD simulation of my protein in DMSO. I used the force
>> field ffG53a6 and did the energy minimization after solvating the 
>> protein in
>> DMSO box.
>> But after solvating in DMSO, the structure is changing. My protein is a
>> homodimer and the loop at the dimer interface is converting into a sheet.
>> Please suggest where I am going wrong since the structure shouldnot 
>> change
>> after solvation.
> 
> You're not giving nearly enough detail (what is the dmso/water ratio? 
> what is your .mdp file?) etc.
> 
> In any case, it wouldn't be the first time that simulations and 
> experiments disagree. How do you *know* that structure shouldn't change? 
> Have you tried using another force field, like OPLS?
> 

This might just be a visualization artifact, something that gets posted here 
routinely.  Some slight structural changes may have occurred during EM, such 
that the visualization program guess sheet instead of loop.  53A6 does tend to 
favor extended structures, but I would only suggest something is wrong if (1) a 
real simulation is conducted and the spurious secondary structure persists and 
(2) real analysis is done (like DSSP or STRIDE) to conclude the secondary 
structure, rather than just looking at it, as all visualization software uses 
different heuristics to assign structures.  It does not make for convincing 
evidence.

-Justin

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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

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