Re: [gmx-users] g_hbond -contact option
Besides used for h-bond, g_hbond can be used for determine whether the distance has fallen into a range (with -nocontact and -r and -r2). g_dist is not good for calculate for distance between two atoms but g_mindist can perform this job well. Actually, because of a compulsive input of tpr file, g_dist has less use than g_mindist when coming to mere distance calculation. Regards, Yang Ye On 11/22/2006 5:46 PM, andrea carotti wrote: Hi all, I have found this interesting option in g_hbond, and I would like to know something more about it. How does it work? Which is the difference with other tools like g_dist? Thanks to all Andrea ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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 mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] g_hbond -contact option
If I'm not mistaken, g_dist deals with the center of mass of two groups, wheras g_hbond -contact is all about the contacts of individual atoms belonging to the two (or one) groups. g_hbond -contact acts just like g_hbond does without the -contact flag, except it ingores the angle criterion for hydrogen bonds. There is now also the option of providing a second distance for assuming a two step interaction process: A + B <=> A- - -B <=> AB, where the middle state is the two species being within the longer, but not within the shorter range (for example B being in the second coordination shell of A). This resembles the hydrogen bond kinetics assumed for the calculations of rate constants of hydrogen bonding in g_hbond, which is why the kinetics of the contacts may also be calculated using hte same scheme when two distances are provided to the program. If you are about to use the -contact flag I strongly suggest you make sure you have the latest gromax version installed, since it contains some important bugfixes for the contact analysis. The -r2 option also requires the latest version. /Erik Marklund - Original Message - From: "andrea carotti" <[EMAIL PROTECTED]> To: Sent: Wednesday, November 22, 2006 10:46 AM Subject: [gmx-users] g_hbond -contact option Hi all, I have found this interesting option in g_hbond, and I would like to know something more about it. How does it work? Which is the difference with other tools like g_dist? Thanks to all Andrea ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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 mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] g_hbond -contact option
If I'm not mistaken, g_dist deals with the center of mass of the two groups chosen, whilst g_hbond -contact is all about the distances of individual atoms of the two/one group(s). g_hbond -contact works just like g_hbond, except that it ignores the angle criterion for hydrogen bonds. You can also provide a second distance using the -r2 option, assuming a two step interaction process. I strongly suggest using the latest version of gromacs when using g_hbond -contact, since there were a bunch of bugfixes made not too long ago. /Erik Marklund - Original Message - From: "andrea carotti" <[EMAIL PROTECTED]> To: Sent: Wednesday, November 22, 2006 10:46 AM Subject: [gmx-users] g_hbond -contact option Hi all, I have found this interesting option in g_hbond, and I would like to know something more about it. How does it work? Which is the difference with other tools like g_dist? Thanks to all Andrea ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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 mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] g_hbond -contact option
Hi all, I have found this interesting option in g_hbond, and I would like to know something more about it. How does it work? Which is the difference with other tools like g_dist? Thanks to all Andrea ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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
