Re: [gmx-users] extract chain information in xtc file
Dear Tina, No need to extract subtrajectories, just create index concerning the separated chains you want to use, and perform the calculation in gromacs. Happy modelling! Stéphane Le 26/03/2019 à 14:13, tina-meryl.am...@ibcp.fr a écrit : Hello, I barely discover Gromacs and I have to use it to study trajectory results, so I wanted to know if it was possible from an xtc file to generate several xtc files, one for each chain of the molecule that we want to study, (in order to retrieve information and perform calculations) and if it is possible, how? I found several information for concatenation or even to cut a simulation of time N in several simulations of time n, but I do not find anything concerning a possible cut according to the chains of the molecule. Thanking you in advance for your answer. -- Lecturer, UFIP, UMR 6286 CNRS, Team Protein Design In Silico UFR Sciences et Techniques, 2, rue de la Houssinière, Bât. 25, 44322 Nantes cedex 03, France Tél : +33 251 125 636 / Fax : +33 251 125 632 http://www.ufip.univ-nantes.fr/ - http://www.steletch.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.
Re: [gmx-users] extract chain information in xtc file
Hi Make use of gmx make_ndx option. Please refer the manual to use it. You can define your chain there and extract it separately On Tue 26 Mar, 2019, 6:49 PM , wrote: > Hello, > I barely discover Gromacs and I have to use it to study trajectory > results, so I wanted to know if it was possible from an xtc file to > generate several xtc files, one for each chain of the molecule that we want > to study, (in order to retrieve information and perform calculations) and > if it is possible, how? I found several information for concatenation or > even to cut a simulation of time N in several simulations of time n, but I > do not find anything concerning a possible cut according to the chains of > the molecule. > > Thanking you in advance for your answer. > -- > 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.
[gmx-users] extract chain information in xtc file
Hello, I barely discover Gromacs and I have to use it to study trajectory results, so I wanted to know if it was possible from an xtc file to generate several xtc files, one for each chain of the molecule that we want to study, (in order to retrieve information and perform calculations) and if it is possible, how? I found several information for concatenation or even to cut a simulation of time N in several simulations of time n, but I do not find anything concerning a possible cut according to the chains of the molecule. Thanking you in advance for your answer. -- 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.
