Re: [AMBER] post-simulation thermodynamic integration calculations

From: David A Case <>
Date: Fri, 9 Nov 2018 08:26:04 -0500

On Thu, Nov 08, 2018, Veenis, Andrew Jay wrote:
>When performing TI, the dV/dL calculations are run during the
>simulations. Is there any way to perform the calculations after the
>simulations have been completed based on the trajectory and prmtop
>files? I'm interested in making a modification to the trajectories and
>performing the calculations again.

This depends on what sort of mixed potential energy surface you are using.

If you have linear mixing (no soft-core option), then dV/dl is just V1-V0.
So, you could use cpptraj or the imin=5 option in sander to compute both V1
and V0 (using whatever modifications to the prmtop files you wish), then
subtract the two values for each snapshot. I'm not aware of any "automated"
script that does this, but it seems pretty straightforward. (Note that I've
never done it myself, so I could be missing something....)

If you are using softcore mixing, I don't see any easy way to do this, since I
think it would require modifications deep inside the TI code.


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Received on Fri Nov 09 2018 - 05:30:02 PST
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