problems with rerun using dcd

Hey Everybody,

I was trying to rerun a simulation via:

rerun trajectory.dcd dump x y z box no format molfile dcd

and got the Error:

No suitable molfile plugin found (…/reader_molfile.cpp:88)

I also get the Error for .xtc files. All files are created by LAMMPS e.g. “dump 1 all dcd 100 test.dcd”
So it seems that for writing out MOLFILE works.

I have compiled the 15. May 2015 version of LAMMPS and the VMD-1.9.1 version.
Also i have recompiled LAMMPS with the VMD-1.9.2 version.
Changed molfile_SYSINC = to molfile_SYSINC = /home/micha/progs/lib/vmd/plugins/include
added -Ldir to molfile_SYSPATH = -Ldir
Nothing helps to get rid of the error. VMD is 64bit (LAMMPS should be 64 bit too, i guess)
Please help me. I have no clue what i"m doing wrong (beside of using dcd files o0), because it seems to work for writing out dcd.

addition:
i have also problems to write out dcd with the molfile command:
dump 5 all molfile 100 test1.dcd format dcd
No suitable molfile plugin found (…/dump_molfile.cpp:105)

so the problem seems to be finding the molfile files.

but if there is a way to dump dcd without molfile (or at least not specify it in the command, which i used) can i rerun it with some other commands then “… format molfile dcd” ?

Best Regards

Micha

Axel can comment. LAMMPS writes dump dcd files itself,

w/out the molfile plug-in. But no one has written native
code to read DCD dump files that way - we rely on the molfile
plug-in for taht. Both errors you are showing look

they are going thru molfile. So if you don’t have DCD support

in your molfile installation, I’m guessing that’t the issue.

steve

Hey Everybody,

I was trying to rerun a simulation via:

rerun trajectory.dcd dump x y z box no format molfile dcd

and got the Error:

No suitable molfile plugin found (../reader_molfile.cpp:88)

I also get the Error for .xtc files. All files are created by LAMMPS e.g.
"dump 1 all dcd 100 test.dcd"
So it seems that for writing out MOLFILE works.

no. this doesn't use molfile. you don't use the molfile dump style,
but the dcd dump style, which is a standalone implementation of a dcd
writer (only).

I have compiled the 15. May 2015 version of LAMMPS and the VMD-1.9.1
version.
Also i have recompiled LAMMPS with the VMD-1.9.2 version.
Changed molfile_SYSINC = to molfile_SYSINC =
/home/micha/progs/lib/vmd/plugins/include
added -Ldir to molfile_SYSPATH = -Ldir

this is not really needed since the molfile ABI has not changed from
the version of the VMD plugin header files included in the LAMMPS
distribution.

Nothing helps to get rid of the error. VMD is 64bit (LAMMPS should be 64 bit
too, i guess)
Please help me. I have no clue what i"m doing wrong (beside of using dcd
files o0), because it seems to work for writing out dcd.

the error message says it all.

No suitable molfile plugin found (../reader_molfile.cpp:88)

that means LAMMPS cannot file any suitable plugin in the directory
path that you have specified. by default that is the current directory
only. if you have your molfile plugins located elsewhere, you have
either specify the path or copy the necessary plugin into the current
working directory.

addition:
i have also problems to write out dcd with the molfile command:
dump 5 all molfile 100 test1.dcd format dcd
No suitable molfile plugin found (../dump_molfile.cpp:105)

so the problem seems to be finding the molfile files.

exactly.

but if there is a way to dump dcd without molfile (or at least not specify
it in the command, which i used) can i rerun it with some other commands
then "... format molfile dcd" ?

if you do it correctly, it will work. i suggest you have a closer look
at the documentation for the molfile dump style.

axel.

First of all thanks Steve and Alex for the fast answers!

Just as fast feedback for others that will maybe have the same problems like me in the future:

I could solve the problem by adding the location of the pluginfile to the rerun-command:

First of all thanks Steve and Alex for the fast answers!

Just as fast feedback for others that will maybe have the same problems like
me in the future:

I could solve the problem by adding the location of the pluginfile to the
rerun-command:

rerun trajectory.dcd dump x y z box no format molfile dcd
.:/home/soft/vmd/vmd-1.9.1/plugins/LINUXAMD64/molfile/

please note that this is the documented behavior.

sadly i wasn't able to set the molfile_SYS* Variables in a way that it works
without the additional path.

this *cannot* work, since plugins are loaded at runtime and only one
plugin can be loaded at a time. linking the static plugin library
would require *much* deeper changes to the LAMMPS code. what the
USER-MOLFILE plugin uses from a VMD installation are only the headers,
and that is only needed, then the plugin ABI is different from the one
described in the headers bundled with LAMMPS.

again, this is all mentioned in the documentation.

axel.