you should go down the list and use all the tools, and use some from seperate software. In my experience, the trjconv gets rid of say 4-5 crazy single points in a graph based on a single point where one of the atoms or residues involved moves between planes, which averidge out in a gaussian distribution, but it removes these. Somone e.lse here probably has better contributions though. It is hard to say without seeing the raw data though.
Stephan Watkins
Gesendet: Montag, 08. September 2014 um 10:25 Uhr
Von: "Ca C." <devi...@hotmail.com>
An: "gromacs.org_gmx-users@maillist.sys.kth.se" <gromacs.org_gmx-users@maillist.sys.kth.se>
Betreff: [gmx-users] g_mindist for hydrophobic interactions
Von: "Ca C." <devi...@hotmail.com>
An: "gromacs.org_gmx-users@maillist.sys.kth.se" <gromacs.org_gmx-users@maillist.sys.kth.se>
Betreff: [gmx-users] g_mindist for hydrophobic interactions
Dear All,
I have to verify if some hydrophobic residues, during the simulation, conserve their interactions and make a "cross talk" for receptor's transactivation.
Is g_mindist a good tool for this purpose? Do you have more suggestions?
Moreover, should I use trjconv for pbc treatment before running g_mindist?
Thank you in advance
--
Gromacs Users mailing list
* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
I have to verify if some hydrophobic residues, during the simulation, conserve their interactions and make a "cross talk" for receptor's transactivation.
Is g_mindist a good tool for this purpose? Do you have more suggestions?
Moreover, should I use trjconv for pbc treatment before running g_mindist?
Thank you in advance
--
Gromacs Users mailing list
* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
-- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
