Re: [AMBER] more efficient TI rerun over existing trajectory

From: David A Case <>
Date: Tue, 29 Oct 2019 08:42:47 -0400

On Mon, Oct 28, 2019, 杨明俊 wrote:

>3. Using trajectories generated in step (2), the individual frames were
>extracted into the .inpcrd files using PARMED. Based on the individual
>coordinate files, (1) change vdw parameters of L0 or L1, (2) regenerate
>the prmtop file (i.e. the new Hamiltonian), (3) recompute the energies
>for each of the coordinate files using the new prmtop file and the same
>setting of TI to get the new energies.

I'm a little lost here: it sounds like you are changing vdw parameters
and re-writing the prmtop file "based on the individual coordinate
files". Doesn't the change in vdw only need to be done once, and then
the new prmtop file can be used to process all of the frames? (Maybe
that is what you meant to say, or I could easily be misunderstanding
your workflow.)

>From what I am doing now, step 3 is too time consuming. I am wondering if
>there is an alternative way to do this energy rerun more efficiently? I
>tried imin=5 with sander.MPI. However, I cannot have sander.MPI read the
>PMEMD generated trajectories with TI.

This is certainly a use case where porting the imin=5 functionality from
sander to pmemd would be useful. cpptraj has a general energy
functionality, but I don't think(?) it supports the pmemd TI model.

Bottom line is that I don't have any immediate suggestions for speeding
things up (unless you are actually creating new prmtop files more often
than you really need to.) Others on the list might have some
suggestions here.


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Received on Tue Oct 29 2019 - 06:00:05 PDT
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