**From:** Giacomo Fiorin (*giacomo.fiorin_at_gmail.com*)

**Date:** Wed Nov 17 2021 - 12:31:47 CST

**Next message:**Ashutosh Shandilya: "Re: colvars: Too many iterations in routine jacobi."**Previous message:**Ashutosh Shandilya: "Re: colvars: Too many iterations in routine jacobi."**In reply to:**Ashutosh Shandilya: "Re: colvars: Too many iterations in routine jacobi."**Next in thread:**Ashutosh Shandilya: "Re: colvars: Too many iterations in routine jacobi."**Reply:**Ashutosh Shandilya: "Re: colvars: Too many iterations in routine jacobi."**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

There *were* multiple RMSD computations, because that's how the distances

between path frames are computed.

You are also omitting several warnings above, btw. One was "Please check

your configuration or increase restraint on z(σ)". What did you do there?

I don't know where you got the PDB structures from, but I recommend that

you load them in VMD and compute the RMSD of the coordinates of your

simulation with respect to each. All RMSDs need to be well defined in

order to be able to compute the path variable derived from them.

Giacomo

On Wed, Nov 17, 2021 at 12:55 PM Ashutosh Shandilya <scfbioiitd_at_gmail.com>

wrote:

*> Thanks for your reply, As I understand I should consider the selection
*

*> which has only moderate change. First step itself gives this problem so I
*

*> have not calculated the RMSD. I have a string of pdbs from PNEB path and I
*

*> want to have a pmf that's why I am using abf. So the selected atoms have
*

*> lots of transformation. So what are the options.
*

*>
*

*> Many thanks,
*

*> Ashutosh
*

*>
*

*> On Wed, Nov 17, 2021 at 11:28 AM Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
*

*> wrote:
*

*>
*

*>> This message is the key:
*

*>> colvars: This is usually the result of an ill-defined set of atoms for
*

*>> rotational alignment (RMSD, rotateReference, etc).
*

*>>
*

*>> If the structure of the group of atoms changes too much, it becomes
*

*>> possible that a pure rotation is not the transformation that minimizes the
*

*>> RMSD, but another transformation does (e.g. rotation + reflection across a
*

*>> plane).
*

*>>
*

*>> You do not need to change the time step, but instead pick a selection
*

*>> that is guaranteed to have only moderate changes in structure. Practically
*

*>> speaking, the RMSD should remain much lower than the radius of gyration.
*

*>>
*

*>> If you compute that RMSD in VMD you will have a similar problem, just
*

*>> with a different outcome because the numerical algorithm is different.
*

*>>
*

*>> Giacomo
*

*>>
*

*>> On Wed, Nov 17, 2021 at 11:03 AM Ashutosh Shandilya <scfbioiitd_at_gmail.com>
*

*>> wrote:
*

*>>
*

*>>> I am running ABF and getting this error.
*

*>>>
*

*>>> Frame index: 32 ; optimal RMSD = 4.87456
*

*>>> Frame index: 31 ; optimal RMSD = 4.87456
*

*>>> Frame index: 30 ; optimal RMSD = 4.87456
*

*>>> Frame index: 29 ; optimal RMSD = 4.87456
*

*>>> Frame index: 28 ; optimal RMSD = 4.87456
*

*>>> colvars: Prepared sample and gradient buffers at step 0.
*

*>>> colvars: Too many iterations in routine jacobi.
*

*>>> colvars: This is usually the result of an ill-defined set of atoms for
*

*>>> rotational alignment (RMSD, rotateReference, etc).
*

*>>> colvars: Too many PFATAL ERROR: Error in the collective variables module
*

*>>> (see above for details)
*

*>>> FATAL ERROR: Error in the collective variables module (see above for
*

*>>> details)
*

*>>>
*

*>>> I have used different timesteps but still I am getting this error. Any
*

*>>> suggestions?
*

*>>>
*

*>>> Many thanks
*

*>>>
*

*>>
*

**Next message:**Ashutosh Shandilya: "Re: colvars: Too many iterations in routine jacobi."**Previous message:**Ashutosh Shandilya: "Re: colvars: Too many iterations in routine jacobi."**In reply to:**Ashutosh Shandilya: "Re: colvars: Too many iterations in routine jacobi."**Next in thread:**Ashutosh Shandilya: "Re: colvars: Too many iterations in routine jacobi."**Reply:**Ashutosh Shandilya: "Re: colvars: Too many iterations in routine jacobi."**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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