Hello, I was wondering if someone can help me with a general genbox question. I have been using the command line:
genbox -ci octanol.gro -nmol 1000 -box 5 5 5 -o prop_1000.gro to fill a box with 1000 molecules of octanol. With the smaller n-alcohols, it worked fine but as I started using 1-butanol, 1-pentanol, (longer carbon chains) up to octanol, Gromacs sometimes ends the command with a 'Killedin-Solvent overlap' line at the very end. Sometimes increasing the box size helped, but for 1-pentanol, even 7 7 7 box size didn't work. Also, do these killed runs take up some sort of space. My memory space decreases a little bit even on failed runs. Thanks. -- Best regards, Fabian F. Casteblanco Rutgers University -- Chemical Engineering PhD Student C: +908 917 0723 E: [email protected] -- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
