[gmx-users] simulation at higher temperatures
arunjones.kumar89 at gmail.com
Mon Aug 29 15:49:36 CEST 2011
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 ,
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).
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.
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)
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.
Arun Kumar Somavarapu
Center for Bioinformatics
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