Hi,
I recommend looking at the Supporting Information of the following paper:
https://pubs.acs.org/doi/abs/10.1021/ct400862k
There are complete sample scripts for post-processing M-REMD trajectories.
What I think you are looking for is the 'ensemble' keyword, which will read
in, sort, and process ensembles of trajectories at the same time.
You set the path of the lowest numbered trajectory out of all of your
replicas (here I use file.000) and it will automatically search for the
rest of the files based on the numeric extension.
parm file.parmtop
ensemble rundir_1/file.mdcrd.000
ensemble rundir_2/file.mdcrd.000
...(usually I image and strip out waters here to decrease file size)
trajout output.mdcrd
The resulting output trajectories will be sorted by your two replica
dimensions as described in the Cpptraj logfile, and you will get all
combinations of dimensions.
If you *only* want to generate specific combinations of your 2 dimensions,
you can use the remdtraj and remdtrajidx keywords:
trajin rundir_1/file.mdcrd.000 remdtraj remdtrajidx 1,4 (where these match
the replica dimensions of interest)
I recommend reading the Cpptraj output closely so you can verify that it is
doing what you think it is doing, and you are getting the replica
dimensions you wanted.
-Christina
On Wed, Apr 25, 2018 at 5:58 AM, Jason Ku Wang <jwang198.stanford.edu>
wrote:
> Hi AMBER Community!
>
> I have thoroughly appreciated the help in getting M-REMD set up!
>
> I now have trajectory (.mcrd) files generated by 2D M-REMD using
> temperature and Hamiltonian dimensions and was hoping to stitch together
> trajectories based on a unique Hamiltonian/temperature combination/pairing.
>
> I was successful in doing this for the case of 1D temperature-based REMD
> using the *remdtrajtemp *keyword. On page 560 in the AMBER16 manual (
> http://ambermd.org/doc12/Amber16.pdf), there is also described a
> *remdtrajidx
> *keyword for the Hamiltonian dimension I presume.
>
> I was wondering if it would be possible use the two keywords in tandem to
> extract a Hamiltonian/temperature pairing?
>
> Thanks so much for the help!
> Jason
>
> --
> Jason Wang
> Stanford University, Class of 2018
> jwang198.stanford.edu
> ᐧ
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
--------------------------------------------------------------
Christina Bergonzo
Research Chemist
NIST/IBBR NRC Postdoctoral Researcher
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Received on Wed Apr 25 2018 - 06:00:08 PDT
