[gmx-users] Error after trjconf processing

James Starlight jmsstarlight at gmail.com
Fri May 3 15:17:05 CEST 2013 

Mark,


but if I run npt equilibration onto minimized structure (without
velocities)  without definition of the new velocities in the npt.mdp file

gen_vel = No

I noticed that in npt.gro file velocities present. Have it been assigned
inspite on
gen_vel = No in mdp?


James

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

> EM has no velocities, by definition. Does the EM mdrun write a .gro file
> with velocities? If so, that's a bug.
>
>
> On Fri, May 3, 2013 at 2:51 PM, James Starlight <jmsstarlight at gmail.com
> >wrote:
>
> > 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).
>
>
> Huh? After EM there should be no velocities, and you should instruct the
> grompp before your equilibration to generate new ones regardless.
>
>
> > Should I re-assign
> > velocities for each conformer (addition nvt run) to fix it ?
> >
>
> There seems to be no purpose to trying to start a new simulation from some
> configuration, doing EM on it, and then trying to equilibrate starting with
> the pre-EM velocities (even if it is possible, which I do not think it
> should be). The energy distributions are guaranteed to be mutually
> inconsistent.
>
> Mark
>
>
> >
> > 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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