From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Mon Jun 26 2017 - 11:32:58 CDT
Hi Francesco, when distances between groups of atoms are involved, it is
really important to check that the PBCs are the same in both VMD and NAMD.
Giacomo
On Mon, Jun 26, 2017 at 12:24 PM, Francesco Pietra <chiendarret_at_gmail.com>
wrote:
> I also run the same ABF (rmsd all atoms of the ligand less methyl
> hydrogens) with colvar "r" = 18.9 from cv printframe (unlike the directly
> measured 27.6 with previous ABFs). In all cases, I took the colvars values
> from the last frame of the 58.2ns MD, not averages along the whole
> simulation)
>
>
> Main< (Conformation:5xxf-SAA1) 28 % cv printframe
>> 0 1.88926419197828e+01 5.22845307973583e+01
>> -3.39612142392650e+01 9.26730407864645e+00 1.01135055762437e+02
>> -5.05311208874754e+01 0.00000000000000e+00 0.00000000000000e+00
>>
>> >Main< (Conformation:5xxf-SAA1) 29 %
>>
>> >Main< (Conformation:Bound_5xxf-SAA1-allH_except_methyl_H) 33 % cv
>> printframelabels
>> # step r Theta
>> Phi Psi theta
>> phi RMSD r_RMSD
>>
>
> The immediate (step 0) error was again atoms moving too fast, this time
> one heavy atom and one H-atom of the ligand.
>
> f
>
> ---------- Forwarded message ----------
> From: Francesco Pietra <chiendarret_at_gmail.com>
> Date: Mon, Jun 26, 2017 at 12:28 PM
> Subject: Fwd: Atoms too fast/periodic cell too small with ABF
> protein-ligand
> To: NAMD <namd-l_at_ks.uiuc.edu>
>
>
> I must add that the attempted ABF was "Conformation:Bound". For rmsd for
> the ligand I had chosen all heavy atoms.
> By choosing all atoms of the ligand, except hydrogens at the methyl
> groups, the simulation also crashed at the first step, this time for two H
> atoms of the protein, one (HG1) very far from the ligand, the other one
> (HA) close to the ligand.
>
> With "Conformation:Unbound" the ABF went to completion without errors.
>
> Hope this helps suggesting what to do.
>
> As I said, there was no problem with MD equilibration for this system, at
> the same ts=1.0fs, along a trajectory of during 58.2ns.
>
> francesco
>
>
> ---------- Forwarded message ----------
> From: Francesco Pietra <chiendarret_at_gmail.com>
> Date: Sun, Jun 25, 2017 at 12:56 PM
> Subject: Atoms too fast/periodic cell too small with ABF protein-ligand
> To: NAMD <namd-l_at_ks.uiuc.edu>
>
>
> Hello:
>
> I am attempting a protein-ligand ABF, following the 2017 tutorial, by
> using a 58.2ns problemless equilibrated system (ts=1.0 fs, bond restriction
> on water only) in a TIP3P water box on a main pure-CPU cluster. Rather
> large protein, organic ligand as accurately parameterized as I could, by
> fitting torsions and water interaction.
>
> I am experiencing immediate "atoms moving too fast" (two H atoms of the
> ligand) when using a linux 4-core cpu desktop, or "periodic cell has become
> too small" on a linux GPU workstation. At the moment I have no access to
> the cluster.
>
> I used ts=1.0 fs, i.e. no bond restriction, except for TIP3P water, as in
> the equilibration.
>
> As a possible cause, that I was unable to verify, is the setting of Euler
> and polar angle in the colvars definition. That is , I used the following
> values from "cv printframe"
>
> >Main< (Conformation:5syf-SAA1) 28 % cv printframe
>> 0 1.88926419197828e+01 5.22845307973583e+01
>> -3.39612142392650e+01 9.26730407864645e+00 1.01135055762437e+02
>> -5.05311208874754e+01 0.00000000000000e+00 0.00000000000000e+00
>>
>
> by discarding the first two, and using the directly measured intercenter
> distance of 27.6A in place of 18.89 from printframe, i.e., as follows:
>
>
> harmonic {
> colvars r
> forceConstant 0.0
> centers 27.6 # OK measured
> }
>
>
> harmonic {
> colvars Theta
> forceConstant 0.0
> centers 52.3 # from printframe
> }
>
>
> harmonic {
> colvars Phi
> forceConstant 0.0
> centers -40.0 # from printframe
> }
>
>
> harmonic {
> colvars Psi
> forceConstant 0.0
> centers 9.27 # from printframe
> }
>
>
> harmonic {
> colvars theta
> forceConstant 0.0
> centers 101.1 # from printframe
> }
>
>
> harmonic {
> colvars phi
> forceConstant 0.0
> centers -50.5 # from printframe
> }
>
> Should this assignment of colvars be correct, where to look for the causes
> of the instability of the system?
> I must confess that I am the first time at such an ABF beyond the tutorial
>
> Thanks for advice
>
> francesco pietra
>
>
>
-- Giacomo Fiorin Associate Professor of Research, Temple University, Philadelphia, PA Contractor, National Institutes of Health, Bethesda, MD http://goo.gl/Q3TBQU https://github.com/giacomofiorin
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