[gmx-users] Box Exploding Error

Hello All, First, for this question I am referring to GROMACS 3.3.3. I have thoroughly read the archives for errors on why a simulation box might explode. My simulations require that I bring the N and C terminal ends of a ~20 amino acid peptide as close together as possible. To do this, I am us

[gmx-users] Box Exploding Error

I would like to thank everyone for their help. Several individuals responded to my initial post. The consensus seemed to be to use distance restraints. My question is, because distance restraints creates penalties if the distance between two atoms EXCEEDS UPPER BOUNDS, wouldn't that apply more fo

Re: [gmx-users] Box Exploding Error

VENKATESH HARIHARAN wrote: Hello All, First, for this question I am referring to GROMACS 3.3.3. I have thoroughly read the archives for errors on why a simulation box might explode. My simulations require that I bring the N and C terminal ends of a ~20 amino acid peptide as close together

Re: [gmx-users] Box Exploding Error

VENKATESH HARIHARAN wrote: Hello All, First, for this question I am referring to GROMACS 3.3.3. I have thoroughly read the archives for errors on why a simulation box might explode. My simulations require that I bring the N and C terminal ends of a ~20 amino acid peptide as close together a

Re: [gmx-users] Box Exploding Error

VENKATESH HARIHARAN wrote: I would like to thank everyone for their help. Several individuals responded to my initial post. The consensus seemed to be to use distance restraints. My question is, because distance restraints creates penalties if the distance between two atoms EXCEEDS UPPER BOUND