handle folders with several simulations

[kain88-de]

I sometimes get several simulations of colleagues that are all in one folder

sim
+-- foo.01.xtc
+-- foo.02.xtc
+-- foo.03.xtc
+-- foo.pdb

My current approach is to move these into separate folders but I would like it I can also tell a Sim that there is more then one simulation in that folder. All simulations have exactly the same setup so I treat it as an ensemble in my analysis instead of a single simulation.

I know I just copy them to different directories and then create sims in them I'm just curious is such a workflow would be possible with mdsynthesis.

[dotsdl]

A Sim doesn't care where the files live that its UniverseDefinition points to, so you could create a bunch of Sim objects anywhere in your filesystem and then define their universes as normal:

import mdsynthesis as mds

sourcedir = mds.Tree('sim')

for traj in sourcedir.glob(*.xtc):
    s = mds.Sim("sim_{}".format(traj.name.split('.')[1]))
    s.universedef.topology = sourcedir['foo.pdb'].abspath
    s.universedef.trajectory = traj.abspath

This will create sim_01, sim_02, and sim_03 in the current directory, and each one will have its universe definition set up as I think you want.

Although MDS works just fine with this approach, in practice I think it works better when the files for a given simulation all reside in that Sim object's tree, since then it's easier to do things like:

import mdsynthesis as mds
import gromacs

b = mds.discover()

# if the xtc files are inside the top level of each Sim, we could grab them
# all like this
xtcs = b.glob('*.xtc')

# let's make a trajectory for each with a coarser timestep
for xtc in xtcs:
    gromcs.trjconv(f=xtc.abspath,
                            o=xtc.parent["{}_dt1ps.xtc".format(xtc.name.partition('.xtc')[0])],
                            dt=1)

since you don't have to grab these files outside of the tree and make sense of which corresponds to what Sim, but it will all technically still work.

[kain88-de]

yup that works thanks