Thanks again. On Wednesday, 31 May 2017 11:01:22 UTC-4, Christoph Junghans wrote: > > 2017-05-31 8:06 GMT-06:00 M. Chakraborty <[email protected] <javascript:>>: > > > 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] <javascript:>. > > To post to this group, send email to [email protected] > <javascript:>. > > 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.
