Re: [gmx-users] Re: editconf -d

2006-07-20 Thread David van der Spoel
Isabella Daidone wrote: Hi, this is what is written in one of the options in editconf: " -[no]c bool no Center molecule in box (implied by -box and -d)". Moreover, in the mailing list you can find discussion about this topic with version 3.2 and David said it was a bug (that -d -c did no

Re: [gmx-users] Re: editconf -d

2006-07-20 Thread X.Periole
On Thu, 20 Jul 2006 10:24:25 +0200 (CEST) Isabella Daidone <[EMAIL PROTECTED]> wrote: Hi, this is what is written in one of the options in editconf: " -[no]c bool no Center molecule in box (implied by -box and -d)". Now you mention it ! did you try a two step process: 1) center (-c),

Re: [gmx-users] Re: editconf -d

2006-07-20 Thread Isabella Daidone
Hi, this is what is written in one of the options in editconf: " -[no]c bool no Center molecule in box (implied by -box and -d)". Moreover, in the mailing list you can find discussion about this topic with version 3.2 and David said it was a bug (that -d -c did not really center). So I w

Re: [gmx-users] Re: editconf -d

2006-07-20 Thread X.Periole
HI Isabelle, I try again, just to know if it is not true that -d implies centering... Hi, when using editconf -d with gromacs version 3.3, it seems that the protein is not at the center but at the corner of the box. In gromacs version 3.3, does option -d in editconf really imply that th

[gmx-users] Re: editconf -d

2006-07-20 Thread Isabella Daidone
I try again, just to know if it is not true that -d implies centering... Hi, when using editconf -d with gromacs version 3.3, it seems that the protein is not at the center but at the corner of the box. In gromacs version 3.3, does option -d in editconf really imply that the protein will be c