Hi Tom, Thanks for the tip. It worked on the command line and I had 3000 frames. But when I fed the file to VMD, it showed only 1800 frames!? Although the initial and final configurations looked correct. I still am not sure what possibly goes wrong!?
Payman On Mon, 2009-11-02 at 10:50 +0000, TJ Piggot wrote: > You should use the -settime option, I think it should solve your problem. > > Tom > > --On Monday, November 02, 2009 00:21:31 -0800 Payman Pirzadeh > <[email protected]> wrote: > > > 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 > > > > ---------------------- > TJ Piggot > [email protected] > University of Bristol, UK. > > _______________________________________________ > 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
