Re: [gmx-users] Error on Box Length when adding ions (gromacs 4.5.3/Charmm27/Tip3p)

X Rules wrote: > > There was a bug in an early 4.0.x feature that box vectors were not properly > written to .pdb files (CRYST line), but this was obviously fixed months, if not > a year or more, ago. Gromacs tools are expected to handle numerous file types > effortlessly, so using .gr

RE: [gmx-users] Error on Box Length when adding ions (gromacs 4.5.3/Charmm27/Tip3p)

> > There was a bug in an early 4.0.x feature that box vectors were not properly > written to .pdb files (CRYST line), but this was obviously fixed months, if > not > a year or more, ago. Gromacs tools are expected to handle numerous file > types > effortlessly, so using .gro is certainly

Re: [gmx-users] Error on Box Length when adding ions (gromacs 4.5.3/Charmm27/Tip3p)

X Rules wrote: > The error would imply that the box you have set up is < 2.0 nm, given the > cutoffs here. How did you define the box (editconf command)? What is your box > size (last line of the .gro file or in the header of a .pdb)? > > -Justin okey.. I got it under control. The pro

RE: [gmx-users] Error on Box Length when adding ions (gromacs 4.5.3/Charmm27/Tip3p)

> The error would imply that the box you have set up is < 2.0 nm, given the > cutoffs here. How did you define the box (editconf command)? What is your > box > size (last line of the .gro file or in the header of a .pdb)? > > -Justin okey.. I got it under control. The problem was. 1. crea

Re: [gmx-users] Error on Box Length when adding ions (gromacs 4.5.3/Charmm27/Tip3p)

.gro file or in the header of a .pdb)? -Justin > Date: Wed, 17 Nov 2010 13:09:32 -0500 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] Error on Box Length when adding ions (gromacs 4.5.3/Charmm27/Tip3p) > > > > X Rules wrote

[gmx-users] Error on Box Length when adding ions (gromacs 4.5.3/Charmm27/Tip3p)

= xyz ; Periodic Boundary Conditions (yes/no) Hope you can locate my error here!! > Date: Wed, 17 Nov 2010 13:09:32 -0500 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] Error on Box Length when adding ions (gromacs > 4.5.3/

Re: [gmx-users] Error on Box Length when adding ions (gromacs 4.5.3/Charmm27/Tip3p)

X Rules wrote: I am having problems with grompp with my system. I am using Gromacs 4.5.3 FF = Charmm27 beta WT = TIP3P (recommended and its claimed its not too different than Charmms TIP3P) during minimization with pbc, I get the error about box length being small if I add neutralizing io

[gmx-users] Error on Box Length when adding ions (gromacs 4.5.3/Charmm27/Tip3p)

I am having problems with grompp with my system. I am using Gromacs 4.5.3 FF = Charmm27 beta WT = TIP3P (recommended and its claimed its not too different than Charmms TIP3P) during minimization with pbc, I get the error about box length being small if I add neutralizing ions (I do not get t