Hi,
Thanks for the heads-up. One more question. So, I looked up the box info
into the topology.prmtop:
%FLAG BOX_DIMENSIONS
%FORMAT(5E16.8)
9.00000000E+01 6.11010000E+01 5.99640000E+01 6.29031000E+01
and , thus, I used this in cpptraj :
parm topology.prmtop
trjain trajectory.mdcrd 219 219 1
box x 61.10 y 59.96 z 62.90 alpha 90.0 beta 90.0 gamma 90.0
trajout 220th_restart.rst7 restart
run
the MD through sander now starts because there is the box, however,
is the box info in the topology file correct, or it needs some correction
factors ?
Cheers,
Manuele
Il giorno ven 22 mag 2020 alle ore 16:56 Daniel Roe <daniel.r.roe.gmail.com>
ha scritto:
> Hi,
>
> Thanks for the files. So at first I thought there was a bug in
> cpptraj, but it turns out that even though the trajectory has the
> 'cell_lengths' etc variables, they are empty (all zeroes)! This is
> part of the output from 'ncdump -v cell_lengths minimization.mdcrd':
> ```
> data:
>
> cell_lengths =
> 0, 0, 0,
> 0, 0, 0,
> ```
> The angles are also zero. Cpptraj sees this and thinks because all the
> lengths and angles are zero, there's no box (because effectively there
> really isn't a box). I should probably have a warning printed there.
>
> So it seems the problem is actually somewhere in sander. If you know
> the dimensions of your box (I think I remember your simulation was
> NVT), you can add the box information back using cpptraj with the
> 'box' command.
>
> Hope this helps,
>
> -Dan
>
> On Fri, May 22, 2020 at 9:59 AM emanuele falbo <falbo.emanuele.gmail.com>
> wrote:
> >
> > Dear both,
> >
> > Yeah, that's right. This is a trajectory from the minimization.
> > cell_lengths variable is there when running "$ ncdump -h
> trajectory.mdcrd":
> >
> > double cell_lengths(frame, cell_spatial) ;
> > cell_lengths:units = "angstrom" ;
> >
> > So, there is actually something wrong in reading the trajectory in
> cpptraj.
> >
> > Is there any way I can add the box to the trajectory.mdcrd, and thus
> start
> > the MD with such new box?
> > Also, will it generate unphysical issues, like self-interactions, due to
> > the different PBC?
> >
> > Cheers,
> > Manuele
> >
> > Il giorno ven 22 mag 2020 alle ore 13:32 David A Case <
> > david.case.rutgers.edu> ha scritto:
> >
> > > On Fri, May 22, 2020, Dan Roe wrote:
> > > >
> > > >Is trajectory.mdcrd the trajectory file from the QM/MM simulation?
> Double
> > > >check that box info is there with ‘ncdump -h’ and look for the
> variable
> > > >cell_lengths. If it isn’t there then for some reason box info wasn’t
> > > >written to the trajectory file. If it is there, cpptraj is missing the
> > > info
> > > >somehow.
> > >
> > > Just a note: this is a "trajectory" file from a minimization run, not
> > > from MD. It could be that there is something odd about that code path,
> > > which is rarely used, and probably not tested.
> > >
> > > ....dac
> > >
> > >
> > > _______________________________________________
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> >
> >
> > --
> >
> > *Emanuele Falbo*
> > PhD student
> > Penfold group
> > School of Natural and Environmental Sciences
> > Bedson Building, Newcastle University
> > Newcastle upon Tyne, NE1 7RU
> > w: http://tompenfoldresearch.weebly.com/
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
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>
--
*Emanuele Falbo*
PhD student
Penfold group
School of Natural and Environmental Sciences
Bedson Building, Newcastle University
Newcastle upon Tyne, NE1 7RU
w: http://tompenfoldresearch.weebly.com/
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Received on Sun May 24 2020 - 03:00:03 PDT
