[gmx-users] Error after trjconf processing

[James Starlight]

I've noticed that the minimized conformers no longer has the velocities in
gro file (and npt rus without warnings in that case) in comparison to the
not-minimized structures ( where velocities were present and gromp sent
warnings). All pbc options lare the same for all conformers and box vectors
correctly defined in boundary regions.

But after npt equilibration of the minimized structures ( velocities again
present in the gro file) my system have crushed at the beginning of the
production run. So the problem in the velocities set which wre taken from
the initial pulling run (the same for each conformers). Should I re-assign
velocities for each conformer (addition nvt run) to fix it ?

James

2013/5/3 Mark Abraham <mark.j.abraham at gmail.com>

> On Fri, May 3, 2013 at 11:15 AM, James Starlight <jmsstarlight at gmail.com
> >wrote:
>
> > Mark,
> >
> > thanks for suggestions
> >
> > as I've told previously I've removed pbc via trjconv witout -pbc mol and
> > -pbc
> > nojump flags
>
>
> I didn't see anything like that in this thread...
>
>
> > (the same way I found in Justin's umbrella tutorial where
> > conformers were extracted from pulling trajectory). Might it be source of
> > the some artifacts with pbc ?
> >
>
> Don't know. Look at your files and see what's there :-)
>
>
> > so if I understood correctly subsequent minimization (with maxwarn 1
> flag)
> > restored original pbc (based on box vectors defined in gro file ) because
> > in next production MD there were no warnings
> >
>
> The PBC was always there. The question is likely whether the code assumes
> molecules have coordinates that do not straddle the current box, or not.
> mdrun goes to the expense of ensuring that it does it correctly, but there
> are countless other points where the code may or may not still be doing
> something that was correct at some point in the last 15 years under certain
> assumptions, but may not be correct now or under new conditions...
>
> Mark
>
> 2013/5/3 Mark Abraham <mark.j.abraham at gmail.com>
> >
> > > Trajectory frames written by mdrun are not post-processed to guess how
> > you
> > > would like PBC to be treated for whatever purpose you have next. So if
> a
> > > molecule straddles a periodic boundary given the current center
> position,
> > > that's what it looks like. If there are things you want to do, then
> > there's
> > > the instructions at
> > >
> > >
> >
> http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
> > > .
> > >
> > > In turn, it seems grompp applies a whole collection of basic checks,
> and
> > it
> > > seems that one of them might not be sufficiently PBC-aware. Such checks
> > > appropriate for a normal grompp workflow, where this is the first point
> > the
> > > GROMACS machinery gets to see what you intend to do and is the point
> > where
> > > it can help you ensure sanity. It seems there's room for a small
> > > improvement, too.
> > >
> > > If the subsequent MD works, then you need have no concern, but if you
> > want
> > > to post-process your trjconv frames so that the molecules are whole,
> you
> > > will suppress this warning the "correct" way.
> > >
> > > Mark
> > >
> > > On Fri, May 3, 2013 at 8:18 AM, James Starlight <
> jmsstarlight at gmail.com
> > > >wrote:
> > >
> > > > Dear Gromacs users!
> > > >
> > > > I have performed long md run. From the production trajectory by means
> > of
> > > >
> > > > trjconv -f md_.trr -s cam.tpr  -dt 10 -e 300 -sep -o ./pdbs/.pdb  #
> > > extract
> > > > conformers from first 300 ps each 10ps steps
> > > >
> > > >
> > > > I've extracted 10 conformers in the desired time step
> > > >
> > > > Than when I perform MD on each conformer I obtain error (when I
> loaded
> > in
> > > > grompp  conformer from the initial run I have no such error)
> > > >
> > > > Number of degrees of freedom in T-Coupling group rest is 130551.00
> > > > Largest charge group radii for Van der Waals: 8.895, 7.586 nm
> > > > Largest charge group radii for Coulomb:       8.895, 8.474 nm
> > > >
> > > > WARNING 1 [file ./mdps/minim.mdp]:
> > > >   The sum of the two largest charge group radii (17.368397) is larger
> > > than
> > > >   rlist (1.000000)
> > > >
> > > >
> > > > Finally after minimization of each conformer with the same R_list
> (with
> > > > maxwarn 1 flag) and starting new MD on the minimizing conformer I
> have
> > no
> > > > such error:
> > > > Largest charge group radii for Van der Waals: 0.241, 0.237 nm
> > > > Largest charge group radii for Coulomb:       0.241, 0.237 nm
> > > >
> > > > Why this error have occurred (with no minimized conformers) and how
> it
> > > > could be fixed correctly ?
> > > >
> > > > James
> > > > --
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