Re: [gmx-users] Confusion Regarding Vacuum
[EMAIL PROTECTED] wrote: Dear All, I am a bit confused regarding Vacuum. I wanted to do EM in Vacuum. I think I can proceed either of the below... 1) I create a box (editconf) and place a molecule with out solvent. 2) Never create a box, then proceed other steps as usual like EM etc. Can we call 2nd option also a vacuum and what is more appropriate? A simulation in vacuo requires that you don't put a solvent in. A simulation with PBC requires that you choose the appropriate pbc option in your .mdp file, and also choose a sensible box size, e.g. with editconf. These two are independent choices. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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
Re: [gmx-users] Confusion Regarding Vacuum
On Mon, 26 Nov 2007 18:06:46 +0530 (IST) [EMAIL PROTECTED] wrote: Dear All, I am a bit confused regarding Vacuum. I wanted to do EM in Vacuum. I think I can proceed either of the below... 1) I create a box (editconf) and place a molecule with out solvent. 2) Never create a box, then proceed other steps as usual like EM etc. you should make sure your mdp file specifies no pbc: pbc = none Can we call 2nd option also a vacuum and what is more appropriate? Regards Chandu ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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 - XAvier Periole - PhD NMR & Molecular Dynamics Group University of Groningen The Netherlands http://md.chem.rug.nl/~periole - ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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
