Your second guess is correct! I used grompp to restart (I had thought it might provide me with the chance to change things if needed). I was surprised initially when "cat" command did not work! The number of frames were most of the time less than what it should be. I also checked the 'trjcat -h'. I did not specifically understand how I might be able to get over this issue. Any advices?
Payman -----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of Mark Abraham Sent: Sunday, November 01, 2009 8:37 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] trjcat xtc files Paymon Pirzadeh wrote: > Sorry, > My command line was: > > trjcat_d_mpi -f AFPI_Ih1010_54_58_Npt265_2.xtc > AFPI_Ih1010_54_58_Npt265_3.xtc AFPI_Ih1010_54_58_Npt265_4.xtc > AFPI_Ih1010_54_58_Npt265_5.xtc AFPI_Ih1010_54_58_Npt265_6.xtc -o > AFPI_Ih1010_54_58_Npt265_merged2-6.xtc > > the "_d_mpi" is the suffix used for double precision and parallel > version of the installed gromacs. OK so now we have some idea what you might be trying to do. The most likely causes are that the first few trajectories have no frames, or that each frame in the earlier trajectories is common to one in the last trajectory. This might happen if you were using grompp to do restarts, or have previously assigned duplicate times somehow. If so, find a better workflow in future. Consult trjcat -h for clues on how to get around this. Mark > Payman > > On Mon, 2009-11-02 at 15:08 +1100, Mark Abraham wrote: >> Paymon Pirzadeh wrote: >>> Hello, >>> I am trying to concatenate several xtc files. When I use the trjcat, it >>> only writes the last file into the output file! where the problem could >>> be? >> In your command line. Why didn't you tell us what it was? :-) >> >> Mark >> _______________________________________________ >> gmx-users mailing list [email protected] >> 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 [email protected]. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> > > _______________________________________________ > gmx-users mailing list [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > _______________________________________________ gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php _______________________________________________ gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
