Re: [gmx-users] Restraining atoms

On 5/9/12 11:34 AM, Steven Neumann wrote: Dear Gmx Users, My plane surface is made of atoms. I would like to restrain positions between them so they will move all togehter or create bonds between them. Would you advise how to do this in the easiest way? If you need to restrain positions

Re: [gmx-users] restraining atoms to the plane at the bilayer center: pull code ?

back to the list. Chris. --original message -- Message: 4 Date: Wed, 8 Sep 2010 15:07:15 +0200 From: maria goranovic mariagorano...@gmail.com Subject: Re: [gmx-users] restraining atoms to the plane at the bilayer center:pull code ? To: Discussion list for GROMACS users gmx

Re: [gmx-users] restraining atoms to the plane at the bilayer center: pull code ?

Dear Chris, Thank you for the code. I did check out pull_pbcatomN, and thank you for the heads up that it is a global index. I used a central atom in the box for each of the two groups as pull_pbcatom. After using the code below with a rate constant of ~ 5500 for about 100 ps, I realized that

Re: [gmx-users] restraining atoms to the plane at the bilayer center: pull code ?

maria goranovic wrote: I want to restrain certain atoms of my simulation to the plane perpendicular to the bilayer normal, and at the bilayer center. Can someone please provide a quick guide on how to do this? I read the pull-code options, but restraining to a plane did not seem possible?

Re: [gmx-users] restraining atoms to the plane at the bilayer center: pull code ?

The manual does discuss restraining to a plane, but this must be the plane in which the atom is already present. [ position_restraints ] ; ai functfc ... 3 1 1000 0 0 How about restraining the atom to some other plane? For example, how about restraining a phosphate group initially