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
--
========================================
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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