[gmx-users] MD - analysis

[Justin A. Lemkul]

Kavyashree M wrote:
> Dear Sir,
> 
>   Thanks for your reply.
> 
>     It means "not a number."  I've never seen that before from g_energy,
>     but based on the extremely small error estimates, especially for the
>     temperature, I'd suspect you're using extremely tight coupling which
>     may be causing some error.
> 
> 
> I was thinking such errors come when there are some infinite values.  

Correct.

> This same
> mdp file parameters I have used to run 3 more simulations in different 
> systems.
> But that was all fine, such "nan" error was not present.
>  

What does gmxcheck tell you about the .edr file that is giving weird results? 
Do the plots look normal?  Perhaps a frame got corrupted somewhere along the 
way.  The screen output should print how many frames were considered in the 
analysis; if it does not match your expectations based on nstenergy and the 
length of the simulation then something went wrong.

> 
>     The RMSD presented by g_energy is the standard deviation of the data
>     analyzed. It is unrelated to the RMSD of the protein.
> 
> 
> Yes that is true. I just checked it to make sure that there is no 
> horrible errors in
> the trajectory.
> 
>     In a periodic system, there is no such thing as "inside" and
>     "outside" since the system is infinite.
> 
> 
> Than is true. but why  mentioned is that when we are analyzing we take into
> account only one of the unit cell not infinite. By outside I meant out 
> of the unit
> cell in consideration into a periodic image.
> 

Most analyses do not need re-imaging.  Keeping the protein within the confines 
of one unit cell is typically just a convenience for visualization.

-Justin

>     trjconv -pbc mol -ur compact (and -center if you like).
> 
> 
> Thank you I will try it out.
> 
>     Never used ngmx, but with the trjconv command I've stated everything
>     should show up quite nicely in VMD :)
> 
> 
> Ok thanks. I am new to VMD need to explore it more.
>  
> Thanking you
> With Regards
> M. Kavyashree
> 
> 

-- 
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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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