2017-05-31 8:06 GMT-06:00 M. Chakraborty <[email protected]>: > Since force matching uses the atom trajectory to compute tabulated forces, I > am wondering if csg_fmatch can be used to get a list of forces derived from > the all-atom trajectory but mapped to the coarse-grained particles. I tried No, csg_fmatch cannot do that. csg_fmatch do force matching, meaning it will give you the force table, so that the forces deviate the least (in a least square sense) from the average force on each particle (type and average over the whole trajectory).
> using the --traj-force option for fmatch but it gave an io error. The > description of the --trj-force flag (coarse-grained trajectory containing > forces of already known interactions) is not very clear to me. The manual > does not talk about it in detail either. Initially I tried mapping the The " --trj-force" is part of the hybrid force matching approach, see: <http://dx.doi.org/10.1002/mats.201100011> For information, see <https://groups.google.com/d/msg/votca/gY2qbyvjlMA/y7Gwsysl84oJ> and here: <https://github.com/votca/csg-tutorials/tree/master/hexane/hybrid_force_matching> Basically, it allows you to subtract forces before force matching. > all-atom traj to cg traj using csg_map. But when I am using gmx traj to > extract the forces, the file lists 6000 (fine grain) atom indices instead of > 2000 (coarse grain). Have you generate a new tpr for the coarse-grained topology? By default "gmx traj" will open topol.tpr, which might not be the right topology. You will need to execute gmx like: $ gmx traj -s CGtopol.tpr -f CGTraj.xtc -b 100 -of CGforce.xvg -pbc Christoph > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected]. > To post to this group, send email to [email protected]. > Visit this group at https://groups.google.com/group/votca. > For more options, visit https://groups.google.com/d/optout. -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
