[gmx-users] gromacs versus amber boxsize

I ran the following command in gromacs: editconf -bt dodecahedron -f p61_vac_gro.gro -o p61_vac_dod.gro -d 0.8 The equivalent command in amber: solvateoct p61_vac.pdb TIP3PBOX 8.0 As far as I understand this, both command created a box were the edges are 0.8 nm away from the solute. But the

Re: [gmx-users] gromacs versus amber boxsize -correction-

Hi, On Tuesday, 29. January 2008 13:14, servaas michielssens wrote: I made a mistake in the numbers, but the question remains: I ran the following command in gromacs: editconf -bt dodecahedron -f p61_vac_gro.gro -o p61_vac_dod.gro -d 0.8 With -d and a triclinic box the size of the system in

Re: [gmx-users] gromacs versus amber boxsize

On Tue, 29 Jan 2008 12:57:13 +0100 servaas michielssens [EMAIL PROTECTED] wrote: I ran the following command in gromacs: editconf -bt dodecahedron -f p61_vac_gro.gro -o p61_vac_dod.gro -d 0.8 The equivalent command in amber: solvateoct p61_vac.pdb TIP3PBOX 8.0 As far as I understand this,