[gmx-users] Re: starting temperature equilibration phase

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

[gmx-users] Re: starting temperature equilibration phase

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? -- View this message in context: http://gromacs.5086.x6.nabble.com/starting-temperature-equilibration-phase-tp5010365p501

[gmx-users] Re: starting temperature equilibration phase

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

[gmx-users] starting temperature equilibration phase

Hello, I'm studying a protein in water at 348 K. In the equilibration phase (nvt, 1 ns) the temperature starts at about 348 K, and i can't see the slowly increase of the temperature. I can't understand why the temperature is so high at the beginning. Could anyone help me? Thanks. -- View this

[gmx-users] Re: Adsorption layer of water molecules

But are these modifies just a question about the visualization of the trajectory? Thank you very mych! -- View this message in context: http://gromacs.5086.n6.nabble.com/Adsorption-layer-of-water-molecules-tp5005243p5005358.html Sent from the GROMACS Users Forum mailing list archive at Nabble

[gmx-users] Re: Adsorption layer of water molecules

Thank you very much! But when I use trjconv how you said, the water molecules are still in the cubic form, like in the beginning. Isn't there any problem? -- View this message in context: http://gromacs.5086.n6.nabble.com/Adsorption-layer-of-water-molecules-tp5005243p5005356.html Sent from the

[gmx-users] Re: Adsorption layer of water molecules

Actually, I used trjconv (nojump) and these are the images of the run after the post-processing. I didn't understand very well what you mean with the box vectors of the starting and ending. When I used editconf, it has shown: box vectors : 7.205 10.465 11.742 (nm) new box vectors : 7.589 7.58

[gmx-users] Re: Adsorption layer of water molecules

The increase of the box volume occur in the beginning of the npt equilibration. The analysis of pressure was like that: Pressure nvt = fluctuates between 500 bar Pressure npt = fluctuates 1 bar Pressure in production stage = fluctuates 1 bar Actually, the problem is that water molecules go very f