Re: [gmx-users] Problem with using distance restraints (disre) with PBC

Hi i have modified the src to stop harmonic potentials being put into the graph (as was suggested to me by Berk Hess, see below for the modification you need to make). I would be imagine this is also possible to do for distance/orientation restraints, however i only know a small amount of progr

Re: [gmx-users] Problem with using distance restraints (disre) with PBC

Hi Tom, Have you modified the src? As far as I know this has not been done in 331 or 332. I'm unsure of 333. I would be interested in the patch. As far as I know the problem is due to the the distance/orientation restraints being placed in the bonded graph. There was a bit of chatter on the d

Re: [gmx-users] Problem with using distance restraints (disre) with PBC

I agree with increasing the size of the box (if seeing inconsistent shifts, as i should have mentioned in my previous post) and in this case it is practical to do as the system is quite small. However (just for future reference) if the problem were in a much larger system (as it is in my case)

Re: [gmx-users] Problem with using distance restraints (disre) with PBC

I have had a similar problem with orientation restraints. Are the residues far is space? Are you getting inconsistent shifts? If so - If so re-define your box size so that the shortest box vector is greater than the distance restraint residue + some tolerance. I also noticed - [ distance_res

Re: [gmx-users] Problem with using distance restraints (disre) with PBC

Hi, Firstly I would strongly reiterate what Mark said. I would make sure the distance restraints are causing your problem. Again as Mark said make sure you can simulate your system without the distance restraints, and then I would try to simulate the system with distance restraints and with a

Re: [gmx-users] Problem with using distance restraints (disre) with PBC

Grace Li wrote: Hello, I am having some trouble using distance restraints. My goal is to apply a harmonic potential to the distance between two atoms in a short peptide (35 residues). Doing simulations in vacuo, both of the following techniques worked to restrain the distance. Also, both techniqu

Re: [gmx-users] Problem with using distance restraints (disre) with PBC

Hi, I am sure what exactly you are trying to simulate, but your distances seem a bit large (8.1 nm) for a small peptide. Having your restraints _far_ off may cause a crash. Flemming On 5 Mar 2008, at 17:16, Grace Li wrote: Hello, I am having some trouble using distance restraints. My goal

[gmx-users] Problem with using distance restraints (disre) with PBC

Hello, I am having some trouble using distance restraints. My goal is to apply a harmonic potential to the distance between two atoms in a short peptide (35 residues). Doing simulations in vacuo, both of the following techniques worked to restrain the distance. Also, both techniques worked for simu