From: Ashutosh Shandilya (scfbioiitd_at_gmail.com)
Date: Wed Nov 17 2021 - 11:51:32 CST
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.
On Wed, Nov 17, 2021 at 11:28 AM Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
> 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
> 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.
> On Wed, Nov 17, 2021 at 11:03 AM Ashutosh Shandilya <scfbioiitd_at_gmail.com>
>> 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
>> I have used different timesteps but still I am getting this error. Any
>> Many thanks
This archive was generated by hypermail 2.1.6 : Fri Dec 31 2021 - 23:17:12 CST