Apparently you are right! But my desktop has 4GB RAM, and to be honest, when I load normal trajectories (I know they are smaller in size) but I have not seen such issue in almost 60% increase in RAM occupation by VMD. Normally I load 1000 frames, and now I want 3000 frames. Why should it run to such a strange problem?
On Mon, 2009-11-02 at 18:57 +0100, XAvier Periole wrote: > > On Nov 2, 2009, at 18:13, Paymon Pirzadeh <[email protected]> wrote: > > > 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! > Memory limit? > > > > 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:gmx-users- > >>> [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 > _______________________________________________ > 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
