Hi,
yes I have tried the temperature dependent trajectory which gives the same
number of structures. I think I have found the error
Checking coordinates: remd.mdcrd.001
WARNING in checkCoordinates(), AMBER trajectory file is corrupted: '*'
detected (remd.mdcrd.001)
so when I look into the *mdcrd file
REMD 1 200000 ******** 458.600
* are introduced so it seems that it is skipping the rest of the coordinates
after this?
I have used VMD for the trajectory and I use the prmtop file - what tells me
that there are to few trajectories is when I multiply the number in the
mdin-file and I look at the number of structures written to the mdcrd-file
which are the same number as I would expect from the my input parameter
file.
If I change f.ex
REMD 1 200000 ******** 458.600
to
REMD 1 200000 9999999 458.600
File (test.mdcrd.001) is an AMBER REMD (new format) trajectory, 1 files
total (First index is 001), frames at 300.000000 K will be used, each file
has 20000 sets
the number of sets are increased where is earlier read
File (remd.mdcrd.001) is an AMBER REMD (new format) trajectory, 12 files
total (First index is 001), frames at 300.000000 K will be used, each file
has 19999 sets
So will probably need to change the ***** to a number?
On Mon, Sep 13, 2010 at 1:13 PM, Adrian Roitberg <roitberg.qtp.ufl.edu>wrote:
> Maybe you can try, just ONCE, to write the temperature trajectory from
> the remd trajectory, and see if that mdcrd file behaves 'correctly' ?
>
> Adrian
>
>
> On 9/13/10 1:09 PM, Carlos Simmerling wrote:
> > Amber11 is the latest for sander.
> >
> > so in the ptraj output it says that there are 20,000 frames, and has a
> dot
> > for each? it reads all without error?
> > and you are using the same prmtop to read the output trajectory? is it
> > correct? meaning have you visualized the output trajectory using
> something
> > like VMD, and the frames are correct but there are too few? what it is
> that
> > tells you there are too few frames?
> > thanks, these will help troubleshoot your problem.
> >
> > On Mon, Sep 13, 2010 at 7:04 AM, Jorgen Simonsen<jorgen589.gmail.com
> >wrote:
> >
> >> sure - I am using amber10 and ambertools 1.4 which should be the
> lastest.
> >>
> >> On Mon, Sep 13, 2010 at 12:41 PM, Carlos Simmerling<
> >> carlos.simmerling.gmail.com> wrote:
> >>
> >>> it's not possible to help unless you specify which version of sander
> and
> >>> which version of ptraj/ambertools.
> >>>
> >>> On Mon, Sep 13, 2010 at 6:19 AM, Jorgen Simonsen<jorgen589.gmail.com
> >>>> wrote:
> >>>
> >>>> Hi all,
> >>>>
> >>>> I have performed a remd with a 250.000 number of exchange trials
> during
> >>> the
> >>>> simulation every 0.5 ps. I have set ntwx=5.000 so I would expect
> 25.000
> >>>> structures in my simulation but after processing the data using the
> >>> script
> >>>> to extract the coordinates at different temperatures I get
> >>>>
> >>>> #!/bin/csh
> >>>>
> >>>> ptraj l_dermorphin.prmtop<< EOF
> >>>> trajin remd.mdcrd.001 remdtraj remdtrajtemp 300.0
> >>>> trajout remd.300K.mdcrd nobox
> >>>>
> >>>> distance d1 out dist.300K.dat :1.CA :7.CA
> >>>>
> >>>> go
> >>>> EOF
> >>>> which reads all the output files
> >>>>
> >>>> Processing AMBER REMD trajectory (new format) files remd.mdcrd.001 ->
> >>>> remd.mdcrd.010
> >>>>
> >>>> I only get 19999 structures - when I grep *REMD*' in the mdcrd.001
> file
> >> I
> >>>> get 25.000 lines with REMD as expected. I do not know where my mistake
> >> is
> >>>> any help appreciated
> >>>> _______________________________________________
> >>>> AMBER mailing list
> >>>> AMBER.ambermd.org
> >>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>
> >>> _______________________________________________
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> >>>
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> >>
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> >
>
> --
> Dr. Adrian E. Roitberg
> Associate Professor
> Quantum Theory Project, Department of Chemistry
>
> Senior Editor. Journal of Physical Chemistry.
>
> on Sabbatical in Barcelona until August 2011.
> Email roitberg.ufl.edu
>
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Received on Mon Sep 13 2010 - 05:00:03 PDT
