[gmx-users] oplsaa vs. charmm

[jalemkul at vt.edu]

Quoting simon sham <ssham44 at yahoo.com>:

> Hi,
> Once again, I appreciate all the responses.
> 1. To correct I just had in the previous email. I used GROMOS53ab  
> not CHARMM. My apology.
> 2. At high temperaure, one of the helical turn in a alpha helix (3  
> residues) turns into a coil in GROMOS forcefield throughout the 20ns  
> simulation. It was only slightly distorted in OPLSAA simulation in  
> 20ns.
> 3. The RMSF (backbone) for those 3 residues: 0.3nm in GROMOS vs. 0.1  
> nm in OPLSAA.
>
> As I mentioned, the protein is near its melting temperature,  
> therefore, I am not surprised to see some helix to coil transition  
> or helical distortions. As Justin has suggested, I probably will try  
> to make a longer run to see what will happen.
>

Gromos96 53a6 shows a bias towards extended configurations, thus  
excessively destabilizing helices.  There are recent papers about this  
phenomenon.  Sort of a huge difference between Gromos96 and CHARMM :)

-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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