Hi, I have been creating several .g96 configuration files "by hand" (actually, using a scripting language).
I like .g96 as a configuration file format because it provides 9 decimal places of precision for the x, y, and z coordinates of the position and velocity of atoms in my system -- whereas .gro and .pdb configuration file formats offer much lower precision. My system is crystalline, and I found many months ago that the lower precision offered by .gro and .pdb is not quite enough to achieve the exact bond lengths that I want in my crystal. Many months ago, Professor van der Spoel suggested on this list that I switch to .g96 for my configurations. So for many months I have been successfully using .g96 configurations as input to grompp to make the .tpr files necessary for simulation. Today, however, I am trying to do something somewhat unusual, and I run into an unusual problem. Suppose I have made three .g96 configurations "by hand": conf1.g96, conf2.g96, and conf3.g96. I want to compute the single-point energy of all three configurations. (Why would I want to do this? I have written code in a scripting language to generate frames in which a particular angle is "scanned" from one extreme to the other; I want to use Gromacs to simply compute the single-point energy at each frame in the "scan," without taking any MD moves.) One way to do this might be to run three different zero-step MD simulations, by passing the three configurations separately to grompp, obtaining three separate .tpr files, and passing those three .tpr files to mdrun. But this documentation page http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy warns that zero-step MD simulations have "complications related to catering to possible restarts" and is not recommended. Doing it that way is also a little inconvenient because eventually I will have dozens or hundreds of separate "handmade" .g96 configurations for which to calculate the single-point energy, and running hundreds of zero-step simulations would probably require some sort of bash script. So, my thought is to concatenate the three (or more) .g96 configurations into a single trajectory, and then feed that trajectory to the -rerun switch of mdrun to compute the energy of each frame. My question is, how can I concatenate three (or more) .g96 configurations into a single trajectory of any type? I have tried: trjcat -f conf1.g96 conf2.g96 conf3.g96 -o output.trr But I get this error message: ------------------------------------------------------- Program trjcat, VERSION 4.5.5 Source code file: trxio.c, line: 693 Fatal error: Reading trajectories in .g96 format is broken. Please use a different file format. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- Reading trajectories in .g96 format may be broken, but reading CONFIGURATIONS in .g96 is not broken, as far as I know (I routinely pass g96 configurations to the -c switch of grompp). Is there any other way I can concatenate three (or more) .g96 configurations into a single trajectory of any type (.trr, .xtc, etc) -- WITHOUT going through .gro or .pdb (e.g., by converting from .g96 using editconf), which have lower precision? Thanks so much for your time! Andrew DeYoung Carnegie Mellon University -- 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.
