Re: [gmx-users] Genbox question
Fabian Casteblanco wrote: 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. Generating random boxes in this way requires lots of memory and is prone to failure. A useful strategy is to overestimate the size of the box so that genbox doesn't have to do too many iterations to place all of the molecules, then run a nice, long equilibration to get the box vectors (and therefore density, etc) correct. -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
Re: [gmx-users] Genbox question
Justin A. Lemkul wrote: Fabian Casteblanco wrote: 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. Generating random boxes in this way requires lots of memory and is prone to failure. A useful strategy is to overestimate the size of the box so that genbox doesn't have to do too many iterations to place all of the molecules, then run a nice, long equilibration to get the box vectors (and therefore density, etc) correct. A more reliable method is probably genconf: genconf -f molecule.gro -nbox 10 10 10 -o box.gro You'll get 1000 molecules every time and the box size should be sensible. Then proceed with equilibration. -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