[gmx-users] Constraints not working in pull code (sometimes, sometimes not)

Are you 100% sure that you have the correct index group for your large box? Did you use a .ndx file that you prepared as input to mdrun or did you rely on the creation of a standard group? If you relied on the creation of a standard group, can you please try again with the larger box and a

[gmx-users] Constraints not working in pull code (sometimes, sometimes not)

tests. Chris -- original message -- Re: Constraints not working in pull code (sometimes, sometimes not) Krapnik krapnik at gmail.com Thu Aug 11 09:53:24 CEST 2011 * Previous message: [gmx-users] append files in Gromacs 3.3 * Next message: [gmx-users] Constraints not working in pull

[gmx-users] Constraints not working in pull code (sometimes, sometimes not)

I agree that Justin is probably correct, although constraints should technically work just fine with a highly dynamic reference group. Any problems should show up as the system blowing up, but not in correctly setting the position. I think that the problems can arise, however, when you have

Re: [gmx-users] Constraints not working in pull code (sometimes, sometimes not)

Krapnik wrote: Dear all, we are trying to simulate molecule in specified depth in octanol to calculate logP. for this purpose we have used box with slab of octanol, molecule in specified distance in z-axis and this mdp: integrator = md dt = 0.002 tinit = 0 ns

[gmx-users] Constraints not working in pull code (sometimes, sometimes not)

Dear all, we are trying to simulate molecule in specified depth in octanol to calculate logP. for this purpose we have used box with slab of octanol, molecule in specified distance in z-axis and this mdp: integrator = md dt = 0.002 tinit = 0 nsteps = 5125000