Re: [gmx-users] editconf -d

2011-12-01 Thread Justin A. Lemkul
mohammad agha wrote: Dear Prof. May I know the best quantity for -d option in editconf program? for example for a cubic box consists of 7 water molecules and 500 surfactant molecules with 22 , 022 , 22 box dimensions in x , y and z? If you've got a box built, what's the need for -d?

[gmx-users] editconf -d

2011-12-01 Thread mohammad agha
Dear Prof. May I know the best quantity for -d option in editconf program? for example for a cubic box consists of 7 water molecules and 500 surfactant molecules with 22 , 022 , 22 box dimensions in x , y and z? Best Regards Sara -- gmx-users mailing listgmx-users@gromacs.org http://li

[gmx-users] editconf -d

2011-11-26 Thread mohammad agha
Dear Prof. I have a system consists of 500 surfactants + 61000 water beads + 500 ion in martini force field into cubic box with 20.3*20.3*20.3 dimensions, May I know the best quantity for -d option in editconf program to prevent from artificial forces, please? Best Regards Sara -- gmx-users m

Re: [gmx-users] editconf -d

2006-07-19 Thread rodrid3
==Original message text===On Wed, 19 Jul 2006 10:18:30 EDT Isabella Daidone wrote:-d is not for centering. -d is the distance of the protein from the walls of the box.  Hi,when using editconf -d with gromacs version 3.3, it seems that the protein is not at the center but at

[gmx-users] editconf -d

2006-07-19 Thread Isabella Daidone
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 centered or is there still a bug (as in version 3.2.1) or am I missing some