[gmx-users] Form of 10-4 Wall Potential Function.

Could someone clarify the form of the 10-4 potential function used in GROMACS walls? Is it really 10-4, and not 10-4-3? We have tried to create our own 10-4 potential using tables but it doesn't match the results of the built-in GROMACS wall type. ___ g

[gmx-users] 10-4 Wall Potential.

Just wanting to confirm: The potential function for the 10-4 wall in GROMACS is of the form: VLJ = c12*density*pi/(5*r^10) - c6*density*pi/(2*r^4) It is NOT the same as the 10-4-3 function which is also sometimes used to model surface-fluid interactions? Thanks, Travis T. _

[gmx-users] Re: How does MDrun number atoms?

We are using version 3.3. We switched over to 4.0.2 but encountered the 'hanging' problem mentioned by Patrick Fuchs and others and went back. Our version of MPI LAM is 7.1.2. We'll try using openMPI and see if that allows GMX 4.0.2 to run okay. By using gmxdump on our .tpr file, we figured out wh

[gmx-users] How does MDrun number atoms?

Our minimization ended with a large net force on "atom 0." Since there is no atom 0 in our .gro, .top, or .ndx files, is mdrun re-numbering the atoms in our system according to some scheme, or is this an indication that something very wrong is happening? -Travis Trudeau, MSc. student at University

[gmx-users] Combining LJ & Buckingham?

Is there a way within GROMACS to use both Buckingham and Lennard-Jones potentials in the same simulation? So for example water-water could be modelled with LJ and water-solute with Buckingham? ___ gmx-users mailing listgmx-users@gromacs.org http://ww