Re: [gmx-users] printing coords ; energies
Thank you. Sorry for not being clearer. I meant where in the source code are the energy related functions variables? Omer. Koby Levy research group, Weizmann Institute of Science. http://www.weizmann.ac.il/sb/faculty_pages/Levy/ On Thu, Sep 4, 2008 at 16:19, Jochen Hub [EMAIL PROTECTED] wrote: Omer Markovitch wrote: Dear All, I would like to consult you on the following two things: 1) I have a small, preanalysis, routine I would like to run each time a frame is written and added to the trajectory file. After some checking, I believe that, in the file *stat.c*, the routine *void write_xtc_traj(FILE *log,t_commrec *cr, char *xtc_traj,t_nsborder *nsb,t_mdatoms *md, int step,real t,rvec *xx,matrix box,real prec)* is the routine actually printing each frame. Is this true or perhaps I've missed something? 2) Regarding energies - where are the energies stored? I mean the energy per type? The energies of the energy groups (as defined in the mdp file) are stored in the edr file (ener.edr by default). jochen In which file variable is this defined? I understand that these values are printed to the log file (usually named md.log), but I failed to locate the exact functions dealing with this. Thanks, Omer. Koby Levy research group, Weizmann Institute of Science. http://www.weizmann.ac.il/sb/faculty_pages/Levy/ ___ 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 -- Dr. Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de Tel.: +49 (0)551 201-2312 ___ 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 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] printing coords ; energies
Dear All, I would like to consult you on the following two things: 1) I have a small, preanalysis, routine I would like to run each time a frame is written and added to the trajectory file. After some checking, I believe that, in the file *stat.c*, the routine *void write_xtc_traj(FILE *log,t_commrec *cr, char *xtc_traj,t_nsborder *nsb,t_mdatoms *md, int step,real t,rvec *xx,matrix box,real prec)* is the routine actually printing each frame. Is this true or perhaps I've missed something? 2) Regarding energies - where are the energies stored? I mean the energy per type? In which file variable is this defined? I understand that these values are printed to the log file (usually named md.log), but I failed to locate the exact functions dealing with this. Thanks, Omer. Koby Levy research group, Weizmann Institute of Science. http://www.weizmann.ac.il/sb/faculty_pages/Levy/ ___ 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] printing coords ; energies
Omer Markovitch wrote: Dear All, I would like to consult you on the following two things: 1) I have a small, preanalysis, routine I would like to run each time a frame is written and added to the trajectory file. After some checking, I believe that, in the file *stat.c*, the routine *void write_xtc_traj(FILE *log,t_commrec *cr, char *xtc_traj,t_nsborder *nsb,t_mdatoms *md, int step,real t,rvec *xx,matrix box,real prec)* is the routine actually printing each frame. Is this true or perhaps I've missed something? 2) Regarding energies - where are the energies stored? I mean the energy per type? The energies of the energy groups (as defined in the mdp file) are stored in the edr file (ener.edr by default). jochen In which file variable is this defined? I understand that these values are printed to the log file (usually named md.log), but I failed to locate the exact functions dealing with this. Thanks, Omer. Koby Levy research group, Weizmann Institute of Science. http://www.weizmann.ac.il/sb/faculty_pages/Levy/ ___ 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 -- Dr. Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de Tel.: +49 (0)551 201-2312 ___ 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
