dump molfile

Dear LAMMPS users,

I have been trying to set up a dump command to generate PDB files using “dump molfile”. I built LAMMPs executable including user molfile package (in LAMMPS 31 March 2017 version). I found an old case on the same problem on: https://sourceforge.net/p/lammps/mailman/message/34973920/

Unfortunately there is no solution included there, below the information required in that post.

VMD version: 1.9.3

Exact arguments used: dump mf3 all molfile 50 melt3.pdb pdb .:/home/mihasan/lib/vmd/plugins/LINUXAMD64/molfile

Linux version used:

LSB_VERSION=base-4.0-amd64:base-4.0-noarch:core-4.0-amd64:core-4.0-noarch:graphics-4.0-amd64:graphics-4.0-noarch:printing-4.0-amd64:printing-4.0-noarch

Red Hat Enterprise Linux Server release 6.8 (Santiago)

Red Hat Enterprise Linux Server release 6.8 (Santiago)

Dear LAMMPS users,

I have been trying to set up a dump command to generate PDB files using
“dump molfile”. I built LAMMPs executable including user molfile package
(in LAMMPS 31 March 2017 version). I found an old case on the same problem
on: https://sourceforge.net/p/lammps/mailman/message/34973920/

Unfortunately there is no solution included there, below the information
required in that post.

​unfortunately, same as in the e-mail exchange you quoted, there is no
information about *what* doesn't work and how it fails and what kind of
error messages are printed, if any.

VMD version: 1.9.3

Exact arguments used: dump mf3 all molfile 50 melt3.pdb pdb
.:/home/mihasan/lib/vmd/plugins/LINUXAMD64/molfile

Linux version used:

LSB_VERSION=base-4.0-amd64:base-4.0-noarch:core-4.0-amd64:core-4.0-noarch:
graphics-4.0-amd64:graphics-4.0-noarch:printing-4.0-amd64:
printing-4.0-noarch

Red Hat Enterprise Linux Server release 6.8 (Santiago)

Red Hat Enterprise Linux Server release 6.8 (Santiago)

Ldd output of ~/lib/vmd/plugins/LINUXAMD64/molfile/pdbplugin.so

linux-vdso.so.1 => (0x00007ffe83376000)

libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x00007f98f81f7000)

libc.so.6 => /lib64/libc.so.6 (0x00007f98f7e62000)

libm.so.6 => /lib64/libm.so.6 (0x00007f98f7bde000)

/lib64/ld-linux-x86-64.so.2 (0x00007f98f863d000)

libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007f98f79c8000)

I installed the extension at https://sites.google.com/site/akohlmey/software/lammps-plugin , the problem still exists.

​as in my previous response, this is completely pointless.​

Can you please let me know how to fix it? Thank you very much,

​it is next to impossible to provide help without knowing the exact problem.

axel.​

Apologies for not including enough information,

I am just trying to get a dump file in pdb format, so I made a simple simulation of a polymer in a box running in NVT ensemble for 5 steps only (it had no purpose but to get pdb running).

The part of the code where the command is used is given below:

dump A all custom 5 OUTPUTFILE id type x y z #

dump mf3 all molfile 50 melt3.xyz xyz .:/home/mihasan/lib/vmd/plugins/LINUXAMD64/molfile

thermo 10

thermo_style custom step temp pe ke etotal density

run 5

The output seams normal until the command “dump molfile”, an error is generated :

ERROR on proc 0: No suitable molfile plugin found (…/dump_molfile.cpp:105)

Is there anything else I need to provide?

Best regards,

M. Hasan

Apologies for not including enough information,

I am just trying to get a dump file in pdb format, so I made a simple
simulation of a polymer in a box running in NVT ensemble for 5 steps only
(it had no purpose but to get pdb running).

The part of the code where the command is used is given below:

dump A all custom 5 OUTPUTFILE id type x y z #

dump mf3 all molfile 50 melt3.xyz xyz .:/home/mihasan/lib/vmd/
plugins/LINUXAMD64/molfile

thermo 10

thermo_style custom step temp pe ke etotal density

run 5

The output seams normal until the command “dump molfile”, an error is
generated :

ERROR on proc 0: No suitable molfile plugin found (../dump_molfile.cpp:105)

Is there anything else I need to provide?

please check the path to the molfile plugins​ in your input very carefully.
an alternate approach would be to not set the path, but just copy the
desired plugins to the working directory.

you have provided the ldd output for the plugin, it would be nice to
confirm whether your LAMMPS executable is compatible, i.e. also 64-bit and
not 32-bit.

FWIW, your example commands try to output .xyz format file, not .pdb and
those can also be natively generated with the xyz dump style.

axel.

Dear Axel,

Thank you for the immediate response,

The ldd output of serial executable is:

linux-vdso.so.1 => (0x00007ffcf8123000)

libdl.so.2 => /lib64/libdl.so.2 (0x00007fcfefd9f000)

libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x00007fcfefa98000)

libm.so.6 => /lib64/libm.so.6 (0x00007fcfef814000)

libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007fcfef5fe000)

libc.so.6 => /lib64/libc.so.6 (0x00007fcfef269000)

/lib64/ld-linux-x86-64.so.2 (0x00007fcfeffde000)

I copied pdbplugin.so and lammpsplugin.so from VMD to the same folder that has lmp_serial, and changed the command to:

dump mf3 all molfile 50 melt3.pdb pdb .

That made no difference unfortunately.

To be clear, the plugin “lammpsplugin.so” is the one from VMD installation. I saw that it is newer than that at https://sites.google.com/site/akohlmey/software/lammps-plugin

So I assumed installing the older plugin won’t solve the problem. Is that correct?

Best Regards,

M. Hasan

Not the folder of the executable, but the folder of the simulation input.

Axel

Dear Axel,

Thank you for the immediate response,

The ldd output of serial executable is:

linux-vdso.so.1 => (0x00007ffcf8123000)

        libdl.so.2 => /lib64/libdl.so.2 (0x00007fcfefd9f000)

        libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x00007fcfefa98000)

        libm.so.6 => /lib64/libm.so.6 (0x00007fcfef814000)

        libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007fcfef5fe000)

        libc.so.6 => /lib64/libc.so.6 (0x00007fcfef269000)

        /lib64/ld-linux-x86-64.so.2 (0x00007fcfeffde000)

I copied pdbplugin.so and lammpsplugin.so from VMD to the same folder that
has lmp_serial, and changed the command to:

dump mf3 all molfile 50 melt3.pdb pdb .

That made no difference unfortunately.

To be clear, the plugin “lammpsplugin.so” is the one from VMD
installation. I saw that it is newer than that at
https://sites.google.com/site/akohlmey/software/lammps-plugin

So I assumed installing the older plugin won’t solve the problem. Is that
correct?

as mentioned before, ​the location and version of the lammpsplugin.so file
is *completely* irrelevant. it is required to read native LAMMPS trajectory
files into VMD, but that is not what you are trying to do.

axel.

The executable and the simulation input are in the same folder. Anything else I can try?

Best regards,

M. Hasan

The executable and the simulation input are in the same folder. Anything
else I can try?

​there are two more things. lets try the simple one first:
please locate the ​molfile_plugin.h vmdplugin.h files in your VMD
installation and use them to replace the corresponding files in the LAMMPS
distribution and then recompile your lammps executable. there may be a
mismatch of the molfile plugin interface version.

axel.

Thank you for the suggestion.

It didn’t work unfortunately. What can I do next?

Best wishes,

MH

Thank you for the suggestion.

It didn’t work unfortunately. What can I do next?

​please see, if you can install two debugging tools called "strace" and
"ltrace" and use them on your LAMMPS runs.

then please do something like this:

strace -o strace.txt ./lmp_serial -in in.input​

​and:

ltrace -o ltrace.txt ./lmp_serial -in in.input​

​and please send the two files to be off-list via e-mail.

axel.​