Thank you Mark and Chandan. I found two files traj.xtc and traj.trr that were written for the extended simulation and I concatenated those respective files with the previous trajectories.
Sorry to ask this here, but I have posted questions regarding PCA analysis 2 days back and I have not got any reply from the user-list. So, if you people can help me out with this , it will of great help. Here's the query that I posted for the PCA analysis .. I want to perform the dihedral PCA for two residues of a turn region in a protein i.e 4 dihedral angles. I have created an index file for the atoms constituting phi and psi angles for those two residues. But I don't understand what has to be written in covar file .. According to manual it says "covar.ndx, which necessarily contains one group of atom 1 to integer(2*N/3), where N is the number of dihedral angles". This means that covar should contain 1 2 3 (for 4 dihedrals). Here's teh steps that I followed till now. 1. Make an index file for residues 116 , 117 phi-psi angles . Here's its contents : [phi-psi-116-117] 1797 1799 1801 1809 1799 1801 1809 1811 1809 1811 1813 1816 1811 1813 1816 1818 2. used _angle -f mdrun.xtc -n index-dihedral.ndx -or dangle.trr -type dihedral -b 5000 -e 10000 3. trjconv -s mdrun.tpr -f dangle.trr -o resiz.gro -n covar.ndx -e . Here's the content for resiz.gro file : Generated by trjconv : Protein in water t= 0.00000 3 1ALA N 1 -0.234 0.972 0.083 1ALA H1 2 0.997 -0.944 -0.329 1ALA H2 3 -0.017 -1.000 0.000 2.00000 2.00000 2.00000 Why there is alanine here in this file ?? Thanks in advance for help =========== BHARAT On Sat, Nov 23, 2013 at 12:49 AM, Mark Abraham <mark.j.abra...@gmail.com>wrote: > Reading the .log file is sometimes useful ;-) There you will find what > inputs mdrun actually had, and thus decided to do! > > Mark > On Nov 22, 2013 4:11 PM, "Chandan Choudhury" <iitd...@gmail.com> wrote: > > > Dear Bharat, > > > > You can check the time stamp of the trajectory. You can get an idea > whether > > anything was written on it or not. > > > > Chandan > > > > > > -- > > Chandan kumar Choudhury > > NCL, Pune > > INDIA > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.