Re: [gmx-users] oplsaa vs. charmm

between Gromos96 and CHARMM :) -Justin -- 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

Re: [gmx-users] protein-ligand interaction

. 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 -- gmx-users mailing listgmx-users@gromacs.org http

Re: [gmx-users] protein-ligand interaction

S-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 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/g

Re: [gmx-users] histograms

Quoting Nilesh Dhumal : Hello, I trying to run umbrella sampling simulation for system. To get histograms should I make pullx-files.dat with pullx.files and then use g_wham. There is a tutorial that explains all of this: http://www.gromacs.org/Documentation/Tutorials#Pull_Code_and_Umbrella_

Re: [gmx-users] ion jumping out of water box

Quoting ? ?? : Hi all, I have been running simulations of a soluble protein bound to a pair of calcium ions. I have been running this simulation in 4 nano second intervals. everything looks fine until the 14th nano second when one of the ions just jumps out of the water box. pbc-mol does

Re: [gmx-users] histograms

Quoting Nilesh Dhumal : I run the following command. g_wham -it tpr-files.dat -ix pullx-files.dat I am getting only one pick. I have total 20 pullx. files. Why I am getting only one pick instead of multiple. My guess is you're plotting histo.xvg wrong. Try xmgrace -nxy histo.xvg and/or

Re: [gmx-users] histograms

Quoting Nilesh Dhumal : I am using gnuplot I am using following script to plot set term postscript set output "histo.eps" p 'histo.xvg' u 1:2 w l Also attached plot. I don't use gnuplot much, but it seems from your command that you're telling gnuplot to only use the first two columns (1

Re: [gmx-users] perfluorohexane pdb

Quoting ABEL Stephane 175950 : Re hi Marcelo, Below the perfluorohexane molecule in the pdb format construct with the Discovery Studio Visualizer v2.5 REMARK Accelrys Discovery Studio PDB file REMARK Created: Mon Jan 10 20:52:13 Paris, Madrid 2011 HETATM1 C1 0 -11.336