Re: [AMBER] Targeted MD shows blank output file!

From: Jason Swails <>
Date: Wed, 4 Mar 2015 07:53:05 -0500

> On Mar 4, 2015, at 7:21 AM, Pallavi Mohanty <> wrote:
> Thanks Carlos for your valuable input, yes i did a sample run for 50 ps and
> got the results. But with the same input for 10ns, this is the situation.
> FYI, i am running amber 11.11.7 rmsd is the figure for those 30 residues
> mentioned in tgtfitmask.

I have no idea what version of Amber this is supposed to be. But if it *is* Amber 11, I highly recommend updating to AmberTools 14, which includes sander and is available for free download.

That said, if your mdcrd and other files are being written, just not your mdout, that may indicate that the output file buffer isn’t flushing. In which case, by the end of the simulation, the contents to the file should be written (unless for whatever reason the job is killed).

However, I thought that the output file was flushed after mdout writes...

> Moreover i want to pick one intermediate structure
> and yes i am interested to fetch the transition path too. please suggest,
> where i have gone wrong?

Carlos pointed out where you went wrong. Asking the system to go from 11 A RMSD to 0 A RMSD very quickly is almost guaranteed not to work.

I’ll try an analogy: Think of it like a complex maze, in which there is a wall behind you pushing from the start to the end. That wall is the targeted MD restraint energy. What that wall means is that you can’t go *backwards* to find the correct path through the maze if you take a wrong turn somewhere. If that wall moves very quickly, you don’t have much time to survey the maze and pick out the correct pathway. Since there are way more “wrong” ways in this maze that dead-ends in the wrong place, the chances that you’ll get stuck go way up when your wall moves quickly (i.e., when your simulation is short). A slower-moving wall allows you to relax and survey the maze, picking the correct (or at least a much better) way out that will get you to (or close to) the exit.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Wed Mar 04 2015 - 05:00:03 PST
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