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

From: Pallavi Mohanty <>
Date: Wed, 4 Mar 2015 18:35:07 +0530

Thanks Carlos and Jason for your prompt relies!
Do you mean to say that i need to change below mentioned part marked in red
to get the desired output?



  TYPE='TGTRMSD', istep1=1, istep2=4000000, value1=11.7, value2=0.0,

  TYPE='TGTRMSD', istep1=4000000, istep2=5000000, value1=0.0, value2=0.0,



On Wed, Mar 4, 2015 at 6:23 PM, Jason Swails <> wrote:

> > 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.
> HTH,
> Jason
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
> AMBER mailing list

Pallavi Mohanty
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Received on Wed Mar 04 2015 - 05:30:03 PST
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