[gmx-users] editconf -d
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://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] editconf -d
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? The purpose of setting a value with -d is to define a unit cell around a solute such that it does not interact with its periodic image during the simulation. The value is, to some extent, controlled by the cutoff values used during MD. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] editconf -d
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 mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] editconf -d
==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 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 something?ThanksIsabella___gmx-users mailing list gmx-users@gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-usersPlease don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED]Can't post? Read http://www.gromacs.org/mailing_lists/users.php===End of original message text! === ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
