Re: [gmx-users] protein-water distance restraints

2011-10-12 Thread Justin A. Lemkul
arkus *Von:* "Francesco Oteri" *Gesendet:* Oct 12, 2011 6:41:05 PM *An:* gmx-users@gromacs.org *Betreff:* Re: [gmx-users] protein-water distance restraints Dear Markus, If you know the residues composing the cavi

Re: [gmx-users] protein-water distance restraints

2011-10-12 Thread Markus Weingarth
Hi Francesco,Thanks for your answer, but that's not an option for me. I really would like to force the penetreation of a water-molecule into this cavity over the couse of the trajectory.CheersMarkusVon: "Francesco Oteri" Gesendet: Oct 12, 2011 6:41:05 PMAn: gmx-users@gromacs.orgBetreff: Re: [gmx-us

Re: [gmx-users] protein-water distance restraints

2011-10-12 Thread Francesco Oteri
Dear Markus, If you know the residues composing the cavity (and I think you know it), you can simply change the coordinates of the water molecule in the .gro file to move the water in the cavity. Francesco Il 12/10/2011 18:17, Markus Weingarth ha scritto: Dear Gromacs-users, I would like t

[gmx-users] protein-water distance restraints

2011-10-12 Thread Markus Weingarth
Dear Gromacs-users,I would like to force an arbitrary water molcule from the box into an occluded cavity of a membrane-channel. It do not want this water molcule within the cavity at the beginning of the simulation.I though that I could implement intermolecular distance restraints between a water r