[gmx-users] simulation at higher temperatures

[Justin A. Lemkul]

arun kumar wrote:
> 
> Hi friends,
>  
> As a part of my work i have to do simulation at higher temperature (400K 
> or more) to study the folding, unfolding and stability of protein, for 
> that i kept simulation for 3ns at 400k (400k temperature both in 
> equilibration and production) keeping all the other parameters as usual 
> (time step 2fs, explicit solvent model SPC, equilibration with NVT and 
> NPT ensembles for 100ps each  ). the simulation was completed but ,

I doubt any simulation, even of the simplest protein, is "complete" at 3 ns.

> 1. in trajectory i found that protein is comming out of the box (cubic 
> box -d 1.0) i think may be the box size was not sufficient  (and i know 
> that when we increase the temperature the velocity of atoms will increase).

Please see FAQ #3 under the following section:

http://www.gromacs.org/Documentation/FAQs#Analysis_and_Visualization

> 2.  when i save the structure with minimum energy  and saw in pymol i 
> found the side chains, hydrogens was broken through out the protein.

Same as above.

> 3. later i used the command ( trajconv -s md.tpr -f md.trr -o 
> protein.pdb -pbc nojump -dt 10 ) to save the conformations at each 10 ps 
> and to see the conformational changes by playing it as a movie in pymol 
> , but i found a single conformation was just shaking through out the 
> movie (this is happening in normal simulation also)  

Your simulation length is inadequate to view any conformational changes.  These 
types of motions can require hundreds of ns, if not more (depending on the size 
of the protein), to visualize.

-Justin

> 
> later i read in gmx user problems that most of the force field 
> parameters are calculated at room temperature, so in that case what are 
> the parameters and forcefield that we need to fallow for higher 
> temperature simulations.
> 
> so can any one please takes time to explain this, it would be helpful 
> for me to study further.
> 
> Thanking you.
> 
> with regards  
> -- 
> Arun Kumar Somavarapu
> Center for Bioinformatics
> Pondicherry University
> Kalapet
> Puducherry-605014
> 

-- 
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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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