From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Sun Jul 23 2017 - 01:58:42 CDT
In the hope that it turns useful also to the readers, I can add:
> If the number of atoms involved is too few (which ones?)
In this protein-ligand FEP, the reference structure is the ligand for which
/\G0 is sought, with all atoms, except methyl H-atoms (total ca 50 atoms).
> or in general if you come into an issue with linearly-dependent vectors in
> the associated matrix
you have noticed that the error only comes out when RATTLE (ts=2.0fs) is
activated, not at "rigidbons water" ts=1.0fs.
a flexible structure but not one that changes too much internally
the ensemble (protein + ligands) is quite stable in unbiased MD for over
600ns at ts=1.0fs. FF for the ligands was built at the state of the art (ab
initio, fitting of both dihedrals and water interaction). The organic
ligand for which /\G0 is sought has two quite flexible side chains at a
relatively rigid, complex body. During the 600ns MD, the conformation of
the ligand side chains does not visibly change.
On Fri, Jul 21, 2017 at 7:49 PM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
> Hi Francesco, this is an error that occurs in the RMSD fitting -
> orientational alignment routine. If the number of atoms involved is too
> few (which ones?), or in general if you come into an issue with
> linearly-dependent vectors in the associated matrix, the error comes out.
> Ideally, you want more than 4 atoms for an orientational fit, and a
> flexible structure but not one that changes too much internally (i.e.
> protein unfolding would also raise an error).
> On Fri, Jul 21, 2017 at 1:06 PM, Francesco Pietra <chiendarret_at_gmail.com>
>> While running a FEP simulation, RATTLE ts=2.0fs, error at initial stages:
>> colvars: Too many iterations in routine jacobi.
>>> colvars: No such file or directory
>>> FATAL ERROR: Error in the collective variables module: No such file or
>> In contrast, no errors with "rigid bonds water" ts=1.0fs, hence I do not
>> understand which mismatch is alluded to.
>> for advice
>> francesco pietra
> Giacomo Fiorin
> Associate Professor of Research, Temple University, Philadelphia, PA
> Contractor, National Institutes of Health, Bethesda, MD
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