Re: [gmx-users] Replacing molecules in .gro coordinate file
Supposed I have a .gro file of 38 molecules of A which are already in equilibrated conformations. Now I want to transform 15 molecules of A into B therefore I will have the binary mixture of A/B with 13:15 molar ratio in the final structure. How can I do this? Any suggestions will be appreciated. Maybe open A B in vmd together, and then save them as one PDB? Omer. ___ 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
[gmx-users] Replacing molecules in .gro coordinate file
Hello Guys, I am a newbie for GROMACS and MD also. I apologize if this is a stupid question :). Supposed I have a .gro file of 38 molecules of A which are already in equilibrated conformations. Now I want to transform 15 molecules of A into B therefore I will have the binary mixture of A/B with 13:15 molar ratio in the final structure. How can I do this? Any suggestions will be appreciated. Have a great day Waipot ___ 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] Replacing molecules in .gro coordinate file
Waipot Ngamsaad wrote: Hello Guys, I am a newbie for GROMACS and MD also. I apologize if this is a stupid question :). Supposed I have a .gro file of 38 molecules of A which are already in equilibrated conformations. Now I want to transform 15 molecules of A into B therefore I will have the binary mixture of A/B with 13:15 molar ratio in the final structure. How can I do this? Any suggestions will be appreciated. Depending on how different A and B are, you may be able to complete this task with a text editor. If they are very different, I don't know if there is an easy solution apart from rebuilding the system. You could, for example, have a system with 13 A and insert 15 B using genbox -cp a.gro -ci b.gro -nmol 15 -Justin Have a great day Waipot ___ 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 -- Justin A. Lemkul Graduate Research Assistant 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://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
