[gmx-users] Getting error using gmx trjconv
Dear all,I am getting this kind of error : Command line: gmx trjconv -s 148d-wat-0-reduce-oct_GMX-1.gro -f b.tng -o c.tng -fit rot+trans -n test-o.ndx Will write tng: Trajectory file (tng format) WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. WARNING: If there are molecules in the input trajectory file that are broken across periodic boundaries, they cannot be made whole (or treated as whole) without you providing a run input file. Select group for least squares fit Group 0 ( URE) has 4000 elements There is one group in the index Select group for output Group 0 ( URE) has 4000 elements There is one group in the index Reading frame 0 time 1035500.000 Precision of b.tng is 0.001 (nm) --- Program: gmx trjconv, version 2018.3 Source file: src/gromacs/gmxana/gmx_trjconv.cpp (line 1350) Fatal error: Index[3498] 4001 is larger than the number of atoms in the trajectory file (4000). There is a mismatch in the contents of your -f, -s and/or -n files. Thanks and Regards, Saikat Pal -- 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.
Re: [gmx-users] RDF
Dear Vidya.R Its very difficult to answer this question.It depends on your system .If you run more time of your system, RDF will be more smooth Saikat Pal IIT GUWAHATI On Wednesday 12 July 2017, 10:02:30 AM IST, Vidya R <vidyadevi2...@gmail.com> wrote: Hi, I want to calculate RDF of my organic molecule with a solvent. What should be the duration of my simulation? Is 100 ps enough? Thanks, Vidya.R -- 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.
[gmx-users] How to convert AMBER trajectory to Gromacs trajectory
Dear all, I have converted Amber trajectory (.mdcrd ) to Gromacs trajectory (.trr) using Amber 14 cpptraj. But Now I want to convert .trr to .xtc format. I have used this command: trjconv -s output1.pdb -f qdna-1.trr -o md_0_1.xtc -pbc none -ur compact It shows: Last frame -1 time 0.000 Setting output precision to 0.001 (nm) WARNING no output, last frame read at t=0 gcq#131: "You Fill Your Space So Sweet" (F. Apple) output1.pdb=generated by cpptraj please help me out. I am not much familiar with gromacs.I am using gromacs 4.6.7. Thanks and regards, Saikat -- 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.
