I was trying to calculate rmsd for minimized structures in vmd, and when I
choose all the residues of the protein it gave a very high value (16
angstron), that makes no sense with the alignment of both structures.
I'm so sorry, i made a confusion and asked like a problem in gromacs.
Thank you ver
On 8/7/13 2:36 PM, ypca wrote:
Thank you very much for the answers Justin.
I also would like to know if i could calculate RMSD for backbone and side
chains without the hydrogens atoms, is it possible?
Of course. Please refer to basic tutorial material and read in the manual about
index gr
Thank you very much for the answers Justin.
I also would like to know if i could calculate RMSD for backbone and side
chains without the hydrogens atoms, is it possible?
--
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http://gromacs.5086.x6.nabble.com/starting-temperature-equilibration-phase-tp5010365p501
On 8/6/13 2:45 PM, ypca wrote:
Thank you for the help!
I can completely understand you, but what about the simulated annealing,
isn't it automatically for all systems?
No. If you want to perform simulated annealing, use simulated annealing options
(see the manual).
Why the increase of te
Thank you for the help!
I can completely understand you, but what about the simulated annealing,
isn't it automatically for all systems?
Why the increase of temperature is so fast, like in lysozyme tutorial
(http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/06_equil.h
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