Re: [gmx-users] PBC - Protein - ligand

On 8/11/2011 3:17 AM, Steven Neumann wrote: On Mon, Nov 7, 2011 at 2:26 PM, Justin A. Lemkul > wrote: Steven Neumann wrote: Dear Gmx Users, I know that this problem has been discussed may times but I cannot find the solution to get rid o

Re: [gmx-users] PBC - Protein - ligand

Hi Steven, Step 2: Cluster your molecules. This is where you have to forge a reference frame that you can use to remove jumps from your trajectory. If the ligand is not with the protein at the start, you'll have to shift it so that it is. Maybe -pbc cluster is your friend there. I do assume that t

Re: [gmx-users] PBC - Protein - ligand

On Mon, Nov 7, 2011 at 2:26 PM, Justin A. Lemkul wrote: > > > Steven Neumann wrote: > >> Dear Gmx Users, >> I know that this problem has been discussed may times but I cannot find >> the solution to get rid of pbc in my system: protein and ligand. I followed >> the workflow: >> >> 1. First

Re: [gmx-users] PBC - Protein - ligand

Steven Neumann wrote: Dear Gmx Users, I know that this problem has been discussed may times but I cannot find the solution to get rid of pbc in my system: protein and ligand. I followed the workflow: 1. First make your molecules whole if you want them whole trjconv -f md.trr -s md

Re: [gmx-users] PBC - Protein - ligand

Hi Steven, Don't use -ur compact in the first step and see if that solves the problem. Oh, and be sure that the thing is not just diffusing. There was a thread lately where a diffusing ligand drove someone mad trying to remove the 'jumps'. Cheers, Tsjerk On Mon, Nov 7, 2011 at 3:08 PM, Steven

[gmx-users] PBC - Protein - ligand

Dear Gmx Users, I know that this problem has been discussed may times but I cannot find the solution to get rid of pbc in my system: protein and ligand. I followed the workflow: 1. First make your molecules whole if you want them whole trjconv -f md.trr -s md.tpr -pbc whole -ur compact -o