[gmx-users] Re: insert silicon atoms into ice structure
Thanks for reply. I intended to add these silicon atoms into ice structure, the Santan William wrote: Dear GMXusers, I wanna insert several silicon atoms into an ice crystal. I use genbox with a Silicon.pdb, but there's no any silicon atom in the out file. Do I miss anything? Anyone has some comments? Thanks a lot. If zero atoms were inserted, there probably isn't enough space for them in the box. -Justin Best, william -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: insert silicon atoms into ice structure (Justin A. Lemkul)
Thanks for reply. I intended to add some silicon atoms just into ice structure, so the simulation box only containing ice. You said there probably isn't enough space for them in the box. Did you mean I can't insert these atoms into ice structure if the box only containing ice? Is there any other way to insert silicon atoms into a solid ice structure? Thanks a lot. Best, william Santan William wrote: Dear GMXusers, I wanna insert several silicon atoms into an ice crystal. I use genbox with a Silicon.pdb, but there's no any silicon atom in the out file. Do I miss anything? Anyone has some comments? Thanks a lot. If zero atoms were inserted, there probably isn't enough space for them in the box. -Justin Best, william -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: insert silicon atoms into ice structure (Justin A. Lemkul)
Santan William wrote: Thanks for reply. I intended to add some silicon atoms just into ice structure, so the simulation box only containing ice. You said there probably isn't enough space for them in the box. Did you mean I can't insert these atoms into ice structure if the box only containing ice? Well, are there cavities in the ice structure sufficiently large to fit your silicon atoms? Judging by the failure of your approach, I'd say there's not. Is there any other way to insert silicon atoms into a solid ice structure? You could try generating some random configuration of silicon atoms, then: genbox -cp si.pdb -cs ice.pdb You would then, of course, be potentially interrupting the lattice of water molecules if some are deleted due to overlap with your silicon atoms. But as for whether or not that's important, you'll have to decide. -Justin Thanks a lot. Best, william Santan William wrote: Dear GMXusers, I wanna insert several silicon atoms into an ice crystal. I use genbox with a Silicon.pdb, but there's no any silicon atom in the out file. Do I miss anything? Anyone has some comments? Thanks a lot. If zero atoms were inserted, there probably isn't enough space for them in the box. -Justin Best, william -- 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/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/mailing_lists/users.php
