Re: TMD without alignment

From: Jérôme Hénin (
Date: Sun Aug 06 2017 - 04:23:42 CDT


I may not understand exactly what you want to do, but if it is possible at
all, it should be possible using Collective Variable biases: RMSD
coordinates defined precisely the way you mean (the alignement can be
defined separately from the RMSD itself) and moving restraints that can be
fine-tuned, or even scripted if you need complete control of the process.


On 4 August 2017 at 20:27, John Green <> wrote:

> Hi,
> According to the TMD tutorial, in targetted MD you the pathway between the
> aligned structures which is useful in many cases. But is it possible to do
> it without aligning? Basically I mean changing RMSD of two unaligned
> structures from certain amount to zero by TMD.
> Best,
> JJ

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