Force on CG particles

[M. Chakraborty]

I am interested in simulating 2 site coarse-grained representation of methanol. In order to compare how forces are preserved in the CG-representation and the all-atom simulation, I have mapped the all-atom trajectory into CGtraj.xtc using the following command:

csg_map --top topol.tpr --trj traj.trr --out CGTraj.xtc --force --cg methanol.xml

I did mention nstfout in the gromacs mdp file for the all-atom simulation. When I try extracting the forces from the trajectory file with the command:

gmx traj -f CGTraj.xtc -b 100 -of CGforce.xvg -pbc

I get the following error:

Fatal error:
Cannot extract velocities or forces since your input XTC file does not contain them.

I am not sure what I am missing here. I am attaching the xml file. Thanks.

~M. Chakraborty

[Christoph Junghans]

xtc files only store positions, you will need to use a trr file as
output for csg_map.

Christoph
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Christoph Junghans
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[M. Chakraborty]

Thanks for the reply.

[M. Chakraborty]

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 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 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).  

[Christoph Junghans]

2017-05-31 8:06 GMT-06:00 M. Chakraborty <maghe...@gmail.com>:
> 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

[M. Chakraborty]

Thanks again.