Re: [gmx-users] convert B-factor
I know how to calculate, and have calculated the RMSF of two trajectories (of the same molecule), and I want to compare the two RMSFs. I want convert their discrepancy into B-factors. Can you tell me more detailed? -- Original -- From: "Mark Abraham"; Date: Mon, Dec 28, 2009 11:04 AM To: "Discussion list for GROMACS users"; Subject: Re: [gmx-users] convert B-factor AntonioLeung wrote: > Dear all, > I want to convert the difference of two rmsf data sets into B-factor of > a coordinate (to illustrate their difference by coloring the structure > by B-factor), can anyone tell me how to do it? g_rmsf -h Mark -- 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 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] convert B-factor
Dear all, I want to convert the difference of two rmsf data sets into B-factor of a coordinate (to illustrate their difference by coloring the structure by B-factor), can anyone tell me how to do it? Thanks in advance! Antonio-- 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] problem on make_ndx
thanks!! -- Original -- From: "Carsten Kutzner"; Date: Fri, Nov 27, 2009 04:53 PM To: "Discussion list for GROMACS users"; Subject: Re: [gmx-users] problem on make_ndx On Nov 27, 2009, at 9:46 AM, AntonioLeung wrote: > Hi all, > I have a question with make_ndx: how can I make a group with residues: > 133-136 and 159-163 and 170. Can anyone show me the proper command? Hi, there is more information about this available with make_ndx h -> for help The command you are looking for is r 133-136 | r 159-163 | r 170 Carsten -- 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 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] problem on make_ndx
Hi all, I have a question with make_ndx: how can I make a group with residues: 133-136 and 159-163 and 170. Can anyone show me the proper command? Antonio-- 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] how to make a porcupine plot?
Hi, all, I am newcomer of gmx, and I want to know how to make a porcupine plot after a essential MD. I found it looks nicer than linear interpolations between two extremes. Thanks in advance! Atonio-- 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
