VMD-L Mailing List

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Tue Sep 17 2013 - 02:31:30 CDT

Hi John:
My mistake was placing the folded, final pdb into /output. When placed into
the main remd dir,, show_replica.vmd worked also for me.

However, a question on how show_replicas.vmd works. Thus, following your
kind answer, I first carried out a short T-remd on alanin, as provided by
namd_2.9. I used the final namd-provided folded pdb for comparison. in this
case, show_replicas.vmd warned "not converged".

In my, much more computer demanding case (still far from convergence), I
used, for the vmd comparison, just the renamed initial unfolded pdb as a
fake final folded pdb. In this case, show_replicas.vmd did not warned "not
converged". I should conclude that show_replicas.vmd is simply comparing
the starting, unfolded pdb to the final, presumably folded pdb, as
indicated at the foot of the replica exchange conf file.

If my conclusion is correct (hopefully it is not) show_replica.vmd fails to
do the real job. That would be checking whether each replica is equal to
each other, for example assuring that the average structure is the same
from all replicas as a criterion of convergence. Should my conclusion above
be correct, how to provide the final, folded pdb?

Incidentally, as a tip for other guys, I used the same replica exchange
conf file for all restart jobs. That is probably incorrect, as it provides
a single /output, where, within each replica folder, the different restarts
are distinguished by the job number, such as fold_P2i.job0.0.dcd
fold_P2i.job1.0.restart.dcd fold_P2i.job2.0.restart.dcd etc. By doing
so, I could only provide job.0 to show_replicas.vmd, noone of the various
restarts could be examined . Probably a new replica exchange conf file is
needed for each restart, changing in each case the line

set output_root "output/%s/fold_P2i" ; # directories must exist

so that a new output directory is created. Is that correct?

Thanks a lot for any king advice

francesco pietra

On Tue, Sep 17, 2013 at 7:03 AM, John Stone <johns_at_ks.uiuc.edu> wrote:

> Hi,
> Just to track down what's going on here, where did you obtain the
> show_replicas.vmd script you're working with? Is it from the NAMD guide?:
> http://www.ks.uiuc.edu/Research/namd/2.9/ug/node66.html
> Did you try running the exact example described there, or is your problem
> occuring when running your own replica exchange simulations.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Mon, Sep 16, 2013 at 07:49:15PM +0200, Francesco Pietra wrote:
> > h
> > Hello:
> >
> > I was trying to load namd2.9 replicas into vmd with
> >
> > source the replica exchange conf file
> >
> > show_replicas.vmd
> >
> > whereby the starting structure nvt-02.pdb was read and then the dcd
> for
> > job0:
> >
> > ..................
> > ..................
> > Info) Finished with coordinate file nvt-02.pdb.
> > dcdplugin) detected standard 32-bit DCD file of opposite endianness
> > dcdplugin) CHARMM format DCD file (also NAMD 2.1 and later)
> > Info) Using plugin dcd for coordinates from file
> > output/0/fold_P2i.job0.0.dcd
> > Info) Finished with coordinate file output/0/fold_P2i.job0.0.dcd.
> >
> > The final folded structure was also loaded, then, in the tk console
> > appeared
> >
> > can't read "basesel"
> >
> > at a point that the other six jobs had be taken into consideration.
> >
> > I notice from the code:
> >
> > A }
> > A A set fitmolid [mol new $psf_file]
> > A A mol addfile $fit_pdb_file
> > A A set basesel [atomselect $fitmolid $fit_selection_text]
> >
> > }
> >
> > however, I am unable to connect this to the error message.
> >
> > Thanks for advice
> >
> > francesco pietra
>
> --
> NIH Center for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> http://www.ks.uiuc.edu/Research/vmd/
>