Hi Pablo, You can use trjcat to stitch the parts of your trajectory together. A .cpt file contains information about the state, the positions and such. It doesn't contain static information, like residue/atom names, which are needed for a reference structure.
Cheers, Tsjerk On Thu, Nov 22, 2012 at 3:34 PM, Pablo Englebienne <p.englebie...@tudelft.nl > wrote: > Hi all, > > I am planning to run a 100ns simulation by continuing a simulation in > increments of 1ns. After each round, analyses are performed and the > trajectory scrapped. One of the analysis I need to do is mean square > displacement; for this I need a continuous trajectory as provided by > trjconv -pbc nojump. > > The issue that I have is how to make sure that the trajectory stays > continuous across the different time increments. By reading the manual of > trjconv, I found out that "the starting configuration for this procedure is > taken from the structure file, if one is supplied, otherwise it is the > first frame." I thought of using the .cpt file from the previous step as > structure file (trjconv -s) for trjconv, but .cpt is not one of the formats > accepted for that option (only tpr, tpb, tpa, gro, g96, pdb). > > The other issue is that as the dumping of snapshots is performed > frequently (every 100 timesteps) I would be using double precision, so I > would like to use a double-precision structure to do the "nojump" step as > well. A cpt file seems to be perfectly suited for this, as well as a > single-frame trr file, however neither of them is accepted as a structure > file for trjconv. > > My questions are 2: > 1. what would be the best way to ensure a continuous trajectory across > multiple fragments of a trajectory, using double precision? > 2. is there a specific reason why a cpt is not accepted as a structure > file for trjconv -s? > > Thanks for your comments! > > Regards, > Pablo > > -- > > Dr. Pablo Englebienne > Postdoctoral Researcher > > *TU Delft / 3mE / Process & Energy* > /Engineering Thermodynamics (ETh) group/ > > Building 46 > Leeghwaterstraat 44, room 030 > 2628 CA Delft > The Netherlands > > *T* +31 (0)15 27 86662 <tel:+31152786662> > *E* p.englebie...@tudelft.nl > <mailto:p.englebienne@tudelft.**nl<p.englebie...@tudelft.nl> > > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > * Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Biocomputing Group Department of Biological Sciences 2500 University Drive NW Calgary, AB T2N 1N4 Canada -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists