Re: [gmx-users] questions about umbrella sampling tutorial

On 4/5/13 3:29 AM, Albert wrote: Hello: I am trying to do umbrella sampling for a protein/ligand water system these days following Justin's nice tutorial. And I've got some questions: (1) in the tutorial, the small peptide was pulling along Z direction. I am just wondering, will the small p

[gmx-users] questions about umbrella sampling tutorial

Hello: I am trying to do umbrella sampling for a protein/ligand water system these days following Justin's nice tutorial. And I've got some questions: (1) in the tutorial, the small peptide was pulling along Z direction. I am just wondering, will the small peptide be pulled in both +Z and -Z

[gmx-users] questions about umbrella sampling

Dear R-X Gu, I think that you didn't get a reply because you are clearly using gromacs version 3.x and many of us now work with gromacs 4.x. (Note that the .ppa file is gone in gromacs version 4.x and the pull parameters now go into the regular .mdp file). If there is some reason that you

[gmx-users] questions about umbrella sampling

Dear All: I am using umbrella sampling method to calculate potential of mean force and I encountered the following questions: 1, at the *.ppa file, I need to incorporate a parameter indicating the "the position of the pull group will restraint to, relative to the reference group" (i.e., the "pos1

[gmx-users] questions about umbrella sampling

Dear All: I am using umbrella sampling method to calculate potential of mean force and I encountered the following questions: 1, at the *.ppa file, I need to incorporate a parameter indicating the "the position of the pull group will restraint to, relative to the reference group" (i.e., the