[gmx-users] Amber force fields giving LINCS errors

First off I am using gromacs 4.5. I will also post all of my files and errors if they help. If I run a protein in GROMOS96 all my md runs complete succesfully. But if I change to any of the AMBER force fields I get LINCS errors in my positional restraint md

Re: [gmx-users] Amber force fields giving LINCS errors

TJ Mustard wrote: First off I am using gromacs 4.5. I will also post all of my files and errors if they help. If I run a protein in GROMOS96 all my md runs complete succesfully. But if I change to any of the AMBER force fields I get LINCS errors in my positional restraint md run. I

Re: [gmx-users] Amber force fields giving LINCS errors

Of course. I am trying to run the ribosome 30s subunit on gromax 4.5. I chose the AMBER force field since it had the least issues with RNA and that made running pdb2gmx much easier. Everything is fine till I run a md. Below I have attached everything I think is

Re: [gmx-users] Amber force fields giving LINCS errors

My one thought is that it is to large of a system for GROMACS to run it, yet I have run a small protein in GROMOS96-43a1 and it works but not in any of the AMBER force fields. On September 9, 2010 at 9:35 PM TJ Mustard musta...@onid.orst.edu wrote:

Re: [gmx-users] Amber force fields giving LINCS errors

TJ Mustard wrote: snip *Positional restraint mdp file:* define = -DPOSRES constraints = all-bonds integrator = md dt = 0.004 ; ps Unless you're using virtual sites (which, per your commands below, you are not) this time

Re: [gmx-users] Amber force fields giving LINCS errors

On September 9, 2010 at 10:04 PM Justin A. Lemkul jalem...@vt.edu wrote: TJ Mustard wrote: snip *Positional restraint mdp file:* define = -DPOSRES constraints =