[gmx-users] MD - analysis

[Justin A. Lemkul]

Kavyashree M wrote:
> Dear Sir, 
> 
>   May be this protein is a disulphide bonded dimer where both the  monomers
> are identical and only 1 disulphide bond is there between them. But 
> other proteins
> were not like that. May be that is the MAJOR reason for this. but 
> strangely temp, pres,
> vol, density, kinetic, potential and total energy is stable. STRANGE!!
> 

I see no reason why a disulfide would be the cause of this problem.  People 
simulate these types of proteins all the time.  If you know that the minimum 
image convention has been violated, then you know the time at which it occurred 
(from the g_mindist output).  Watch the trajectory and see what is happening then.

-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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