handle folders with several simulations about mdsynthesis HOT 2 CLOSED

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.

from mdsynthesis.

yup that works thanks

from mdsynthesis.